From cdcfb086de9277a1c1b2d8de57ceb78ae8683f53 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Sun, 26 Apr 2020 13:18:54 -0500 Subject: Updated menu --- .../new/javascript/dataset_menu_structure.json | 2655 ++++++++++++++++---- 1 file changed, 2220 insertions(+), 435 deletions(-) diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json index f9bce083..daf818b1 100644 --- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json +++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json @@ -277,6 +277,18 @@ ] }, "CANDLE": { + "Methylation": [ + [ + "423", + "CANDLE_Meth27_0313", + "CANDLE Newborn Cord ILM HumanMethylation27 (Mar13)*" + ], + [ + "422", + "CANDLE_Meth_0313", + "CANDLE Newborn Cord ILM HumanMethylation27 (Mar13) Z-Score*" + ] + ], "Newborn Cord Blood mRNA": [ [ "324", @@ -307,7 +319,7 @@ ] }, "GTEx": { - "Adipose tissue, subcutaneous mRNA": [ + "Adipose Tissue, Subcutaneous mRNA": [ [ "580", "GTEx_log2_Subcu_0314", @@ -319,7 +331,7 @@ "GTEx Human Subcutaneous (Apr14) RPKM" ] ], - "Adipose tissue, visceral mRNA": [ + "Adipose Tissue, Visceral mRNA": [ [ "587", "GTEx_log2_Visce_0314", @@ -873,14 +885,14 @@ ] }, "GTEx_v5": { - "Adipose tissue, subcutaneous mRNA": [ + "Adipose Tissue, Subcutaneous mRNA": [ [ "718", "GTEXv5_AdipSub_0915", "GTEXv5 Human Adipose Subcutaneous RefSeq (Sep15) RPKM log2" ] ], - "Adipose tissue, visceral mRNA": [ + "Adipose Tissue, Visceral mRNA": [ [ "719", "GTEXv5_AdiVis_0915", @@ -1252,253 +1264,857 @@ ] ] }, - "HB": { - "Cerebellum mRNA": [ + "GTEx_v8": { + "Adipose Tissue, Subcutaneous mRNA": [ [ - "326", - "HBTRC-MLC_0611", - "HBTRC-MLC Human Cerebellum Agilent (Jun11) mlratio" + "950", + "GTEXv8_AdipSub_tpm_0220", + "GTEXv8 Human Adipose Subcutaneous RNA-Seq (Feb20) TPM log2" ], [ - "361", - "HBTRC-MLC_N_0611", - "HBTRC-MLC Human Cerebellum Agilent Normal (Jun11) mlratio" + "901", + "GTEXv8_AdipSub_0220", + "GTEXv8 Human Adipose Subcutaneous RNA-Seq (Feb20) log2" + ] + ], + "Adipose Tissue, Visceral mRNA": [ + [ + "951", + "GTEXv8_AdiVis_tpm_0220", + "GTEXv8 Human Adipose Visceral Omentum RNA-Seq (Feb20) TPM log2" ], [ - "362", - "HBTRC-MLC_AD_0611", - "HBTRC-MLC Human Cerebellum Agilent AD (Jun11) mlratio" + "902", + "GTEXv8_AdiVis_0220", + "GTEXv8 Human Adipose Visceral Omentum RNA-Seq (Feb20) log2" + ] + ], + "Adrenal Gland mRNA": [ + [ + "952", + "GTEXv8_AdrGla_tpm_0220", + "GTEXv8 Human Adrenal Gland RNA-Seq (Feb20) TPM log2" ], [ - "363", - "HBTRC-MLC_HD_0611", - "HBTRC-MLC Human Cerebellum Agilent HD (Jun11) mlratio" + "903", + "GTEXv8_AdrGla_0220", + "GTEXv8 Human Adrenal Gland RNA-Seq (Feb20) log2" ] ], - "Prefrontal Cortex mRNA": [ + "Amygdala mRNA": [ [ - "328", - "HBTRC-MLPFC_0611", - "HBTRC-MLC Human Prefrontal Cortex Agilent (Jun11) mlratio" + "956", + "GTEXv8_Amy_tpm_0220", + "GTEXv8 Human Brain Amygdala RNA-Seq (Feb20) TPM log2" ], [ - "367", - "HBTRC-MLPFC_N_0611", - "HBTRC-MLC Human Prefrontal Cortex Agilent Normal (Jun11) mlratio" + "907", + "GTEXv8_Amy_0220", + "GTEXv8 Human Brain Amygdala RNA-Seq (Feb20) log2" + ] + ], + "Anterior Cingulate Cortex mRNA": [ + [ + "957", + "GTEXv8_AntCtx_tpm_0220", + "GTEXv8 Human Brain Anterior cingulate cortex BA24 RNA-Seq (Feb20) TPM log2" ], [ - "368", - "HBTRC-MLPFC_AD_0611", - "HBTRC-MLC Human Prefrontal Cortex Agilent AD (Jun11) mlratio" + "908", + "GTEXv8_AntCtx_0220", + "GTEXv8 Human Brain Anterior cingulate cortex BA24 RNA-Seq (Feb20) log2" + ] + ], + "Aorta mRNA": [ + [ + "953", + "GTEXv8_ArtAor_tpm_0220", + "GTEXv8 Human Artery Aorta RNA-Seq (Feb20) TPM log2" ], [ - "369", - "HBTRC-MLPFC_HD_0611", - "HBTRC-MLC Human Prefrontal Cortex Agilent HD (Jun11) mlratio" + "904", + "GTEXv8_ArtAor_0220", + "GTEXv8 Human Artery Aorta RNA-Seq (Feb20) log2" ] ], - "Primary Visual Cortex mRNA": [ + "Breast - Mammary Tissue mRNA": [ [ - "327", - "HBTRC-MLVC_0611", - "HBTRC-MLC Human Visual Cortex Agilent (Jun11) mlratio" + "969", + "GTEXv8_BrMa_tpm_0220", + "GTEXv8 Human Breast Mammary Tissue RNA-Seq (Feb20) TPM log2" ], [ - "364", - "HBTRC-MLVC_N_0611", - "HBTRC-MLC Human Visual Cortex Agilent Normal (Jun11) mlratio" + "920", + "GTEXv8_BrMa_0220", + "GTEXv8 Human Breast Mammary Tissue RNA-Seq (Feb20) log2" + ] + ], + "Caudate mRNA": [ + [ + "958", + "GTEXv8_BrCa_tpm_0220", + "GTEXv8 Human Brain Caudate basal ganglia RNA-Seq (Feb20) TPM log2" ], [ - "365", - "HBTRC-MLVC_AD_0611", - "HBTRC-MLC Human Visual Cortex Agilent AD (Jun11) mlratio" + "909", + "GTEXv8_BrCa_0220", + "GTEXv8 Human Brain Caudate basal ganglia RNA-Seq (Feb20) log2" + ] + ], + "Cells - EBV-Transformed Lymphocytes mRNA": [ + [ + "970", + "GTEXv8_EBV_tpm_0220", + "GTEXv8 Human Cells-EBV-transformed lymphocytes RNA-Seq (Feb20) TPM log2" ], [ - "366", - "HBTRC-MLVC_HD_0611", - "HBTRC-MLC Human Visual Cortex Agilent HD (Jun11) mlratio" + "921", + "GTEXv8_EBV_0220", + "GTEXv8 Human Cells-EBV-transformed lymphocytes RNA-Seq (Feb20) log2" ] - ] - }, - "HCP": { - "Phenotypes": [ + ], + "Cells - Transformed Fibroblasts mRNA": [ [ - "None", - "HCPPublish", - "HCP Private Phenotypes" + "971", + "GTEXv8_CTF_tpm_0220", + "GTEXv8 Human Cells-Transformed fibroblasts RNA-Seq (Feb20) TPM log2" + ], + [ + "922", + "GTEXv8_CTF_0220", + "GTEXv8 Human Cells-Transformed fibroblasts RNA-Seq (Feb20) log2" ] - ] - }, - "HLC": { - "Liver mRNA": [ + ], + "Cerebellar Cortex mRNA": [ [ - "320", - "HLC_0311", - "GSE9588 Human Liver Normal (Mar11) Both Sexes" + "961", + "GTEXv8_BrCtx_tpm_0220", + "GTEXv8 Human Brain Cortex RNA-Seq (Feb20) TPM log2" ], [ - "384", - "HLCF_0311", - "GSE9588 Human Liver Normal (Mar11) Females" + "912", + "GTEXv8_BrCtx_0220", + "GTEXv8 Human Brain Cortex RNA-Seq (Feb20) log2" + ] + ], + "Cerebellar Hemisphere mRNA": [ + [ + "959", + "GTEXv8_CerH_tpm_0220", + "GTEXv8 Human Brain Cerebellar Hemisphere RNA-Seq (Feb20) TPM log2" ], [ - "383", - "HLCM_0311", - "GSE9588 Human Liver Normal (Mar11) Males" + "910", + "GTEXv8_CerH_0220", + "GTEXv8 Human Brain Cerebellar Hemisphere RNA-Seq (Feb20) log2" ] ], - "Phenotypes": [ + "Cerebellum mRNA": [ [ - "635", - "HLCPublish", - "HLC Published Phenotypes" + "960", + "GTEXv8_BrCe_tpm_0220", + "GTEXv8 Human Brain Cerebellum RNA-Seq (Feb20) TPM log2" + ], + [ + "911", + "GTEXv8_BrCe_0220", + "GTEXv8 Human Brain Cerebellum RNA-Seq (Feb20) log2" ] - ] - }, - "HLT": { - "Lung mRNA": [ + ], + "Colon - Sigmoid mRNA": [ [ - "455", - "GSE23546HLT0613", - "Super Series GSE23546 Whole-Genome GXD Non-Tumorous Human Lung Tissues Affy HuRSTA array (Jun11) RMA" + "972", + "GTEXv8_ColSig_tpm_0220", + "GTEXv8 Human Colon-Sigmoid RNA-Seq (Feb20) TPM log2" ], [ - "454", - "GRNG-GSE23545HLT0613", - "GRNG/GSE23545 Whole-Genome GXD Non-Tumorous Human Lung Tissues Affy HuRSTA array (Jun11) RMA" + "923", + "GTEXv8_ColSig_0220", + "GTEXv8 Human Colon-Sigmoid RNA-Seq (Feb20) log2" ] - ] - }, - "HSB": { - "Amygdala mRNA": [ + ], + "Colon - Transverse mRNA": [ [ - "330", - "KIN_YSM_AMY_0711", - "GN330 Human Amygdala Affy Hu-Exon 1.0 ST (Jul11) Quantile" + "973", + "GTEXv8_ColTra_tpm_0220", + "GTEXv8 Human Colon-Transverse RNA-Seq (Feb20) TPM log2" + ], + [ + "924", + "GTEXv8_ColTra_0220", + "GTEXv8 Human Colon-Transverse RNA-Seq (Feb20) log2" ] ], - "Cerebellar Cortex mRNA": [ + "Coronary mRNA": [ [ - "331", - "KIN_YSM_CBC_0711", - "Human Cerebellar Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + "954", + "GTEXv8_ArtCor_tpm_0220", + "GTEXv8 Human Artery Coronary RNA-Seq (Feb20) TPM log2" + ], + [ + "905", + "GTEXv8_ArtCor_0220", + "GTEXv8 Human Artery Coronary RNA-Seq (Feb20) log2" ] ], - "Dorsolateral Prefrontal Cortex mRNA": [ + "Esophagus - Gastroesophageal mRNA": [ [ - "333", - "KIN_YSM_DFC_0711", - "Human Dorsolateral Prefrontal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + "974", + "GTEXv8_GastJun_tpm_0220", + "GTEXv8 Human Esophagus - Gastroesophageal Junction RNA-Seq (Feb20) TPM log2" + ], + [ + "925", + "GTEXv8_GastJun_0220", + "GTEXv8 Human Esophagus - Gastroesophageal Junction RNA-Seq (Feb20) log2" ] ], - "Hippocampus mRNA": [ + "Esophagus - Mucosa mRNA": [ [ - "337", - "KIN_YSM_HIP_0711", - "Human Hippocampus Affy Hu-Exon 1.0 ST (Jul11) Quantile" + "975", + "GTEXv8_EsoMu_tpm_0220", + "GTEXv8 Human Esophagus-Mucosa RNA-Seq (Feb20) TPM log2" + ], + [ + "926", + "GTEXv8_EsoMu_0220", + "GTEXv8 Human Esophagus-Mucosa RNA-Seq (Feb20) log2" ] ], - "Inferior Temporal Cortex mRNA": [ + "Esophagus - Muscularis mRNA": [ [ - "339", - "KIN_YSM_ITC_0711", - "Human Inferior Temporal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + "976", + "GTEXv8_EsoMus_tpm_0220", + "GTEXv8 Human Esophagus-Muscularis RNA-Seq (Feb20) TPM log2" + ], + [ + "927", + "GTEXv8_EsoMus_0220", + "GTEXv8 Human Esophagus-Muscularis RNA-Seq (Feb20) log2" ] ], - "Medial Prefrontal Cortex mRNA": [ + "Frontal Cortex mRNA": [ [ - "343", - "KIN_YSM_MFC_0711", - "Human Medial Prefrontal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + "962", + "GTEXv8_BrFr_tpm_0220", + "GTEXv8 Human Brain Frontal Cortex BA9 RNA-Seq (Feb20) TPM log2" + ], + [ + "913", + "GTEXv8_BrFr_0220", + "GTEXv8 Human Brain Frontal Cortex BA9 RNA-Seq (Feb20) log2" ] ], - "Mediodorsal Nucleus of Thalamus mRNA": [ + "Heart - Atrial Appendage mRNA": [ [ - "342", - "KIN_YSM_MD_0711", - "Human Mediodorsal Nucleus of Thalamus Affy Hu-Exon 1.0 ST (Jul11) Quantile" + "977", + "GTEXv8_HAA_tpm_0220", + "GTEXv8 Human Heart-Atrial Appendage RNA-Seq (Feb20) TPM log2" + ], + [ + "928", + "GTEXv8_HAA_0220", + "GTEXv8 Human Heart-Atrial Appendage RNA-Seq (Feb20) log2" ] ], - "Orbital Prefrontal Cortex mRNA": [ + "Heart - Left Ventricle mRNA": [ [ - "347", - "KIN_YSM_OFC_0711", - "Human Orbital Prefrontal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + "978", + "GTEXv8_LV_tpm_0220", + "GTEXv8 Human Heart-Left Ventricle RNA-Seq (Feb20) TPM log2" + ], + [ + "929", + "GTEXv8_LV_0220", + "GTEXv8 Human Heart-Left Ventricle RNA-Seq (Feb20) log2" ] ], - "Phenotypes": [ + "Hippocampus mRNA": [ [ - "None", - "HSBPublish", - "HSB Published Phenotypes" + "963", + "GTEXv8_Hip_tpm_0220", + "GTEXv8 Human Brain Hippocampus RNA-Seq (Feb20) TPM log2" + ], + [ + "914", + "GTEXv8_Hip_0220", + "GTEXv8 Human Brain Hippocampus RNA-Seq (Feb20) log2" ] ], - "Posterior Inferior Parietal Cortex mRNA": [ + "Hypothalamus mRNA": [ [ - "338", - "KIN_YSM_IPC_0711", - "Human Posterior Inferior Parietal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + "964", + "GTEXv8_Hiptha_tpm_0220", + "GTEXv8 Human Brain Hypothalamus RNA-Seq (Feb20) TPM log2" + ], + [ + "915", + "GTEXv8_Hiptha_0220", + "GTEXv8 Human Brain Hypothalamus RNA-Seq (Feb20) log2" ] ], - "Posterior Superior Temporal Cortex mRNA": [ + "Kidney mRNA": [ [ - "350", - "KIN_YSM_STC_0711", - "Human Posterior Superior Temporal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + "979", + "GTEXv8_Kidn_tpm_0220", + "GTEXv8 Human Kidney-Cortex RNA-Seq (Feb20) TPM log2" + ], + [ + "930", + "GTEXv8_Kidn_0220", + "GTEXv8 Human Kidney-Cortex RNA-Seq (Feb20) log2" ] ], - "Primary Auditory (A1) Cortex mRNA": [ + "Liver mRNA": [ [ - "329", - "KIN_YSM_A1C_0711", - "Human Primary Auditory (A1) Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + "980", + "GTEXv8_Liv_tpm_0220", + "GTEXv8 Human Liver RNA-Seq (Feb20) TPM log2" + ], + [ + "931", + "GTEXv8_Liv_0220", + "GTEXv8 Human Liver RNA-Seq (Feb20) log2" ] ], - "Primary Motor (M1) Cortex mRNA": [ + "Lung mRNA": [ [ - "341", - "KIN_YSM_M1C_0711", - "Human Primary Motor (M1) Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + "981", + "GTEXv8_Lung_tpm_0220", + "GTEXv8 Human Lung RNA-Seq (Feb20) TPM log2" + ], + [ + "932", + "GTEXv8_Lung_0220", + "GTEXv8 Human Lung RNA-Seq (Feb20) log2" ] ], - "Primary Somatosensory (S1) Cortex mRNA": [ + "Muscle mRNA": [ [ - "349", - "KIN_YSM_S1C_0711", - "Human Primary Somatosensory (S1) Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + "982", + "GTEXv8_MuSk_tpm_0220", + "GTEXv8 Human Muscle-Skeletal RNA-Seq (Feb20) TPM log2" + ], + [ + "933", + "GTEXv8_MuSk_0220", + "GTEXv8 Human Muscle-Skeletal RNA-Seq (Feb20) log2" ] ], - "Primary Visual Cortex mRNA": [ + "Nerve - Tibial mRNA": [ [ - "354", - "KIN_YSM_V1C_0711", - "Human Primary Visual Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + "983", + "GTEXv8_Tib_tpm_0220", + "GTEXv8 Human Nerve-Tibial RNA-Seq (Feb20) TPM log2" + ], + [ + "934", + "GTEXv8_Tib_0220", + "GTEXv8 Human Nerve-Tibial RNA-Seq (Feb20) log2" ] ], - "Striatum mRNA": [ + "Nucleus Accumbens mRNA": [ [ - "351", - "KIN_YSM_STR_0711", - "Human Striatum Affy Hu-Exon 1.0 ST (Jul11) Quantile" + "965", + "GTEXv8_NuAcc_tpm_0220", + "GTEXv8 Human Brain Nucleus accumbens basal ganglia RNA-Seq (Feb20) TPM log2" + ], + [ + "916", + "GTEXv8_NuAcc_0220", + "GTEXv8 Human Brain Nucleus accumbens basal ganglia RNA-Seq (Feb20) log2" ] ], - "Ventrolateral Prefrontal Cortex mRNA": [ + "Ovary mRNA": [ [ - "356", - "KIN_YSM_VFC_0711", - "Human Ventrolateral Prefrontal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + "984", + "GTEXv8_Ov_tpm_0220", + "GTEXv8 Human Ovary RNA-Seq (Feb20) TPM log2" + ], + [ + "935", + "GTEXv8_Ov_0220", + "GTEXv8 Human Ovary RNA-Seq (Feb20) log2" ] - ] - }, - "Islets-Gerling": { + ], + "Pancreas mRNA": [ + [ + "985", + "GTEXv8_Panc_tpm_0220", + "GTEXv8 Human Pancreas RNA-Seq (Feb20) TPM log2" + ], + [ + "936", + "GTEXv8_Panc_0220", + "GTEXv8 Human Pancreas RNA-Seq (Feb20) log2" + ] + ], "Phenotypes": [ [ "None", - "Islets-GerlingPublish", - "Islets-Gerling Phenotypes" + "GTEx_v8Publish", + "GTEx_v8 Phenotypes" ] - ] - }, + ], + "Pituitary Gland mRNA": [ + [ + "986", + "GTEXv8_Pit_tpm_0220", + "GTEXv8 Human Pituitary RNA-Seq (Feb20) TPM log2" + ], + [ + "937", + "GTEXv8_Pit_0220", + "GTEXv8 Human Pituitary RNA-Seq (Feb20) log2" + ] + ], + "Prostate mRNA": [ + [ + "987", + "GTEXv8_Prost_tpm_0220", + "GTEXv8 Human Prostate RNA-Seq (Feb20) TPM log2" + ], + [ + "938", + "GTEXv8_Prost_0220", + "GTEXv8 Human Prostate RNA-Seq (Feb20) log2" + ] + ], + "Putamen mRNA": [ + [ + "966", + "GTEXv8_PutB_tpm_0220", + "GTEXv8 Human Brain Putamen basal ganglia RNA-Seq (Feb20) TPM log2" + ], + [ + "917", + "GTEXv8_PutB_0220", + "GTEXv8 Human Brain Putamen basal ganglia RNA-Seq (Feb20) log2" + ] + ], + "Salivary Gland mRNA": [ + [ + "988", + "GTEXv8_SalGl_tpm_0220", + "GTEXv8 Human Salivary Gland Minor RNA-Seq (Feb20) TPM log2" + ], + [ + "939", + "GTEXv8_SalGl_0220", + "GTEXv8 Human Salivary Gland Minor RNA-Seq (Feb20) log2" + ] + ], + "Skin - Not Sun Exposed (Suprapubic) mRNA": [ + [ + "989", + "GTEXv8_SkN_tpm_0220", + "GTEXv8 Human Skin-Not Sun Exposed-Suprapubic RNA-Seq (Feb20) TPM log2" + ], + [ + "940", + "GTEXv8_SkN_0220", + "GTEXv8 Human Skin-Not Sun Exposed-Suprapubic RNA-Seq (Feb20) log2" + ] + ], + "Skin - Sun Exposed (Lower leg) mRNA": [ + [ + "990", + "GTEXv8_SkS_tpm_0220", + "GTEXv8 Human Skin-Sun Exposed-Lower leg RNA-Seq (Feb20) TPM log2" + ], + [ + "941", + "GTEXv8_SkS_0220", + "GTEXv8 Human Skin-Sun Exposed-Lower leg RNA-Seq (Feb20) log2" + ] + ], + "Small Intestine - Terminal Ileum mRNA": [ + [ + "997", + "GTEXv8_SInt_tpm_0220", + "GTEXv8 Human Small Intestine - Terminal Ileum RNA-Seq (Feb20) TPM log2" + ], + [ + "948", + "GTEXv8_SInt_0220", + "GTEXv8 Human Small Intestine - Terminal Ileum RNA-Seq (Feb20) log2" + ] + ], + "Spinal Cord mRNA": [ + [ + "967", + "GTEXv8_SpCo_tpm_0220", + "GTEXv8 Human Brain Spinal cord cervical c-1 RNA-Seq (Feb20) TPM log2" + ], + [ + "918", + "GTEXv8_SpCo_0220", + "GTEXv8 Human Brain Spinal cord cervical c-1 RNA-Seq (Feb20) log2" + ] + ], + "Spleen mRNA": [ + [ + "991", + "GTEXv8_Sple_tpm_0220", + "GTEXv8 Human Spleen RNA-Seq (Feb20) TPM log2" + ], + [ + "942", + "GTEXv8_Sple_0220", + "GTEXv8 Human Spleen RNA-Seq (Feb20) log2" + ] + ], + "Stomach mRNA": [ + [ + "992", + "GTEXv8_Sto_tpm_0220", + "GTEXv8 Human Stomach RNA-Seq (Feb20) TPM log2" + ], + [ + "943", + "GTEXv8_Sto_0220", + "GTEXv8 Human Stomach RNA-Seq (Feb20) log2" + ] + ], + "Substantia Nigra mRNA": [ + [ + "968", + "GTEXv8_SubN_tpm_0220", + "GTEXv8 Human Brain Substantia nigra RNA-Seq (Feb20) TPM log2" + ], + [ + "919", + "GTEXv8_SubN_0220", + "GTEXv8 Human Brain Substantia nigra RNA-Seq (Feb20) log2" + ] + ], + "Testis mRNA": [ + [ + "993", + "GTEXv8_Test_tpm_0220", + "GTEXv8 Human Testis RNA-Seq (Feb20) TPM log2" + ], + [ + "944", + "GTEXv8_Test_0220", + "GTEXv8 Human Testis RNA-Seq (Feb20) log2" + ] + ], + "Thyroid mRNA": [ + [ + "994", + "GTEXv8_Thy_tpm_0220", + "GTEXv8 Human Thyroid RNA-Seq (Feb20) TPM log2" + ], + [ + "945", + "GTEXv8_Thy_0220", + "GTEXv8 Human Thyroid RNA-Seq (Feb20) log2" + ] + ], + "Tibial mRNA": [ + [ + "955", + "GTEXv8_ArtTib_tpm_0220", + "GTEXv8 Human Artery Tibial RNA-Seq (Feb20) TPM log2" + ], + [ + "906", + "GTEXv8_ArtTib_0220", + "GTEXv8 Human Artery Tibial RNA-Seq (Feb20) log2" + ] + ], + "Uterus mRNA": [ + [ + "995", + "GTEXv8_Ut_tpm_0220", + "GTEXv8 Human Uterus RNA-Seq (Feb20) TPM log2" + ], + [ + "946", + "GTEXv8_Ut_0220", + "GTEXv8 Human Uterus RNA-Seq (Feb20) log2" + ] + ], + "Vagina mRNA": [ + [ + "996", + "GTEXv8_Vag_tpm_0220", + "GTEXv8 Human Vagina RNA-Seq (Feb20) TPM log2" + ], + [ + "947", + "GTEXv8_Vag_0220", + "GTEXv8 Human Vagina RNA-Seq (Feb20) log2" + ] + ], + "Whole Blood mRNA": [ + [ + "998", + "GTEXv8_Wbl_tpm_0220", + "GTEXv8 Human Whole Blood RNA-Seq (Feb20) TPM log2" + ], + [ + "949", + "GTEXv8_Wbl_0220", + "GTEXv8 Human Whole Blood RNA-Seq (Feb20) log2" + ] + ] + }, + "HB": { + "Cerebellum mRNA": [ + [ + "326", + "HBTRC-MLC_0611", + "HBTRC-MLC Human Cerebellum Agilent (Jun11) mlratio" + ], + [ + "361", + "HBTRC-MLC_N_0611", + "HBTRC-MLC Human Cerebellum Agilent Normal (Jun11) mlratio" + ], + [ + "362", + "HBTRC-MLC_AD_0611", + "HBTRC-MLC Human Cerebellum Agilent AD (Jun11) mlratio" + ], + [ + "363", + "HBTRC-MLC_HD_0611", + "HBTRC-MLC Human Cerebellum Agilent HD (Jun11) mlratio" + ] + ], + "Prefrontal Cortex mRNA": [ + [ + "328", + "HBTRC-MLPFC_0611", + "HBTRC-MLC Human Prefrontal Cortex Agilent (Jun11) mlratio" + ], + [ + "367", + "HBTRC-MLPFC_N_0611", + "HBTRC-MLC Human Prefrontal Cortex Agilent Normal (Jun11) mlratio" + ], + [ + "368", + "HBTRC-MLPFC_AD_0611", + "HBTRC-MLC Human Prefrontal Cortex Agilent AD (Jun11) mlratio" + ], + [ + "369", + "HBTRC-MLPFC_HD_0611", + "HBTRC-MLC Human Prefrontal Cortex Agilent HD (Jun11) mlratio" + ] + ], + "Primary Visual Cortex mRNA": [ + [ + "327", + "HBTRC-MLVC_0611", + "HBTRC-MLC Human Visual Cortex Agilent (Jun11) mlratio" + ], + [ + "364", + "HBTRC-MLVC_N_0611", + "HBTRC-MLC Human Visual Cortex Agilent Normal (Jun11) mlratio" + ], + [ + "365", + "HBTRC-MLVC_AD_0611", + "HBTRC-MLC Human Visual Cortex Agilent AD (Jun11) mlratio" + ], + [ + "366", + "HBTRC-MLVC_HD_0611", + "HBTRC-MLC Human Visual Cortex Agilent HD (Jun11) mlratio" + ] + ] + }, + "HCP": { + "Phenotypes": [ + [ + "None", + "HCPPublish", + "HCP Private Phenotypes" + ] + ] + }, + "HLC": { + "Liver mRNA": [ + [ + "320", + "HLC_0311", + "GSE9588 Human Liver Normal (Mar11) Both Sexes" + ], + [ + "384", + "HLCF_0311", + "GSE9588 Human Liver Normal (Mar11) Females" + ], + [ + "383", + "HLCM_0311", + "GSE9588 Human Liver Normal (Mar11) Males" + ] + ], + "Phenotypes": [ + [ + "635", + "HLCPublish", + "HLC Published Phenotypes" + ] + ] + }, + "HLT": { + "Lung mRNA": [ + [ + "455", + "GSE23546HLT0613", + "Super Series GSE23546 Whole-Genome GXD Non-Tumorous Human Lung Tissues Affy HuRSTA array (Jun11) RMA" + ], + [ + "454", + "GRNG-GSE23545HLT0613", + "GRNG/GSE23545 Whole-Genome GXD Non-Tumorous Human Lung Tissues Affy HuRSTA array (Jun11) RMA" + ] + ] + }, + "HSB": { + "Amygdala mRNA": [ + [ + "330", + "KIN_YSM_AMY_0711", + "GN330 Human Amygdala Affy Hu-Exon 1.0 ST (Jul11) Quantile" + ] + ], + "Cerebellar Cortex mRNA": [ + [ + "331", + "KIN_YSM_CBC_0711", + "Human Cerebellar Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + ] + ], + "Dorsolateral Prefrontal Cortex mRNA": [ + [ + "333", + "KIN_YSM_DFC_0711", + "Human Dorsolateral Prefrontal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + ] + ], + "Hippocampus mRNA": [ + [ + "337", + "KIN_YSM_HIP_0711", + "Human Hippocampus Affy Hu-Exon 1.0 ST (Jul11) Quantile" + ] + ], + "Inferior Temporal Cortex mRNA": [ + [ + "339", + "KIN_YSM_ITC_0711", + "Human Inferior Temporal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + ] + ], + "Medial Prefrontal Cortex mRNA": [ + [ + "343", + "KIN_YSM_MFC_0711", + "Human Medial Prefrontal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + ] + ], + "Mediodorsal Nucleus of Thalamus mRNA": [ + [ + "342", + "KIN_YSM_MD_0711", + "Human Mediodorsal Nucleus of Thalamus Affy Hu-Exon 1.0 ST (Jul11) Quantile" + ] + ], + "Orbital Prefrontal Cortex mRNA": [ + [ + "347", + "KIN_YSM_OFC_0711", + "Human Orbital Prefrontal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + ] + ], + "Phenotypes": [ + [ + "None", + "HSBPublish", + "HSB Published Phenotypes" + ] + ], + "Posterior Inferior Parietal Cortex mRNA": [ + [ + "338", + "KIN_YSM_IPC_0711", + "Human Posterior Inferior Parietal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + ] + ], + "Posterior Superior Temporal Cortex mRNA": [ + [ + "350", + "KIN_YSM_STC_0711", + "Human Posterior Superior Temporal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + ] + ], + "Primary Auditory (A1) Cortex mRNA": [ + [ + "329", + "KIN_YSM_A1C_0711", + "Human Primary Auditory (A1) Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + ] + ], + "Primary Motor (M1) Cortex mRNA": [ + [ + "341", + "KIN_YSM_M1C_0711", + "Human Primary Motor (M1) Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + ] + ], + "Primary Somatosensory (S1) Cortex mRNA": [ + [ + "349", + "KIN_YSM_S1C_0711", + "Human Primary Somatosensory (S1) Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + ] + ], + "Primary Visual Cortex mRNA": [ + [ + "354", + "KIN_YSM_V1C_0711", + "Human Primary Visual Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + ] + ], + "Striatum mRNA": [ + [ + "351", + "KIN_YSM_STR_0711", + "Human Striatum Affy Hu-Exon 1.0 ST (Jul11) Quantile" + ] + ], + "Ventrolateral Prefrontal Cortex mRNA": [ + [ + "356", + "KIN_YSM_VFC_0711", + "Human Ventrolateral Prefrontal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + ] + ] + }, + "Islets-Gerling": { + "Islets mRNA": [ + [ + "824", + "UTHSC_HuIslets_Mar17", + "UTHSC Human Islets Affy Human Gene 2.0 ST (Mar17) RMA" + ] + ], + "Phenotypes": [ + [ + "None", + "Islets-GerlingPublish", + "Islets-Gerling Phenotypes" + ] + ] + }, "TIGEM-Retina-RNA-Seq": { "Phenotypes": [ [ @@ -1516,95 +2132,46 @@ ] } }, - "mouse": { - "AIL": { - "Genotypes": [ + "macaque monkey": { + "Macaca-fasicularis": { + "Amygdala mRNA": [ [ - "None", - "AILGeno", - "AIL Genotypes" + "255", + "INIA_MacFas_AMG_RMA_0110", + "INIA Macaca fasicularis Amygdala (Jan10) RMA" ] ], - "Hippocampus mRNA": [ - [ - "874", - "UCSD_AIL_HIP_RNA-Seq_log2_0418", - "UCSD AIL Hippocampus (Apr18) RNA-Seq Log2" - ], + "Brain mRNA": [ [ - "844", - "UCSD_AIL_HIP_RNA-Seq_0418", - "UCSD AIL Hippocampus (Apr18) RNA-Seq" + "251", + "INIA_MacFas_brain_RMA_0110", + "INIA Macaca fasicularis Brain (Jan10) RMA" ] ], - "Phenotypes": [ + "Hippocampus mRNA": [ [ - "653", - "AILPublish", - "AIL Phenotypes" + "254", + "INIA_MacFas_Hc_RMA_0110", + "INIA Macaca fasicularis Hippocampus (Jan10) RMA" ] ], - "Prefrontal Cortex mRNA": [ - [ - "876", - "UCSD_AIL_PFC_RNA-Seq_log2_0418", - "UCSD AIL Prefrontal Cortex (Apr18) RNA-Seq Log2" - ], + "Nucleus Accumbens mRNA": [ [ - "846", - "UCSD_AIL_PFC_RNA-Seq_0418", - "UCSD AIL Prefrontal Cortex (Apr18) RNA-Seq" + "253", + "INIA_MacFas_Ac_RMA_0110", + "INIA Macaca fasicularis Nucleus Accumbens (Jan10) RMA" ] ], - "Striatum mRNA": [ - [ - "875", - "UCSD_AIL_STR_RNA-Seq_log2_0418", - "UCSD AIL Striatum (Apr18) RNA-Seq Log2" - ], - [ - "845", - "UCSD_AIL_STR_RNA-Seq_0418", - "UCSD AIL Striatum (Apr18) RNA-Seq" - ] - ] - }, - "AIL-LGSM-F34-A": { - "Phenotypes": [ - [ - "655", - "AIL-LGSM-F34-APublish", - "AIL F34-A Phenotypes" - ] - ] - }, - "AIL-LGSM-F34-F39-43-GBS": { - "Phenotypes": [ - [ - "654", - "AIL-LGSM-F34-F39-43-GBSPublish", - "AIL F34-F39-43-GBS Phenotypes" - ] - ] - }, - "AIL-LGSM-F34-GBS": { - "Phenotypes": [ - [ - "656", - "AIL-LGSM-F34-GBSPublish", - "AIL F34-GBS Phenotypes" - ] - ] - }, - "AIL-LGSM-F39-43-GBS": { - "Phenotypes": [ + "Prefrontal Cortex mRNA": [ [ - "657", - "AIL-LGSM-F39-43-GBSPublish", - "AIL F39-43-GBS Phenotypes" + "252", + "INIA_MacFas_Pf_RMA_0110", + "INIA Macaca fasicularis Prefrontal Cortex (Jan10) RMA" ] ] - }, + } + }, + "mouse": { "AKXD": { "Genotypes": [ [ @@ -1685,6 +2252,22 @@ ] ] }, + "B6-Lens": { + "Ocular Lens mRNA": [ + [ + "999", + "MouseB6Lens_rma_0220", + "Mouse Ocular Lens Developmental Timecourse (Feb20) RMA" + ] + ], + "Phenotypes": [ + [ + "None", + "B6-LensPublish", + "B6-Lens Phenotypes" + ] + ] + }, "B6BTBRF2": { "Genotypes": [ [ @@ -1720,6 +2303,25 @@ "B6D2Publish", "UTHSC-Glaucoma-Aged-Retina Phenotypes" ] + ], + "Retina mRNA": [ + [ + "803", + "UTHSC_mm9_B6D2_Ret_0916", + "UTHSC B6D2 Retina Affy MoGene 1.0ST (Sep16) Gene Level RMA" + ], + [ + "804", + "UTHSC_mm9_B6D2_RetEx_0916", + "UTHSC B6D2 Retina Affy MoGene 1.0ST (Sep16) Exon Level RMA" + ] + ], + "Retina microRNA": [ + [ + "806", + "UTHSC_mm10_B6D2_Ret_miRNA_1116", + "UTHSC B6D2 Retina Affy miRNA-4.0 (Nov16) RMA" + ] ] }, "B6D2F2": { @@ -1771,6 +2373,28 @@ "B6D2F2-PSU Genotypes" ] ], + "Muscle mRNA": [ + [ + "134", + "PSU-B6D2F2_0812", + "PSU B6D2F2 Muscle Affy Mouse Genome 430 2.0 (Aug12) RMA" + ], + [ + "404", + "PSU-B6D2F2_F0812", + "PSU B6D2F2 Muscle Affy Mouse Genome 430 2.0 (Aug12) RMA Females" + ], + [ + "405", + "PSU-B6D2F2_M0812", + "PSU B6D2F2 Muscle Affy Mouse Genome 430 2.0 (Aug12) RMA Males" + ], + [ + "406", + "PSU-B6D2F2_M2000812", + "PSU B6D2F2 Muscle Affy Mouse Genome 430 2.0 (Aug12) RMA Males Aged 200*" + ] + ], "Phenotypes": [ [ "None", @@ -1906,6 +2530,23 @@ "UCLA BHF2 Liver (June05) mlratio" ] ], + "Muscle mRNA": [ + [ + "203", + "UCLA_BHF2_MUSCLE_FEMALE", + "UCLA BHF2 Muscle Female mlratio*" + ], + [ + "202", + "UCLA_BHF2_MUSCLE_MALE", + "UCLA BHF2 Muscle Male mlratio*" + ], + [ + "168", + "UCLA_BHF2_MUSCLE_0605", + "UCLA BHF2 Muscle (June05) mlratio*" + ] + ], "Phenotypes": [ [ "None", @@ -2090,6 +2731,26 @@ "414", "UCLA_BXD-on_Femur_0113_RSN", "UCLA GSE27483 BXD Only Bone Femur ILM Mouse WG-6 v1.1 (Jan13) RSN" + ], + [ + "464", + "UTHSCWGU88BFMG1013", + "UTHSC WGU88 Male Bone Femur AFFY Mouse Gene ST 2.0 Gene Level (Oct13) RMA" + ], + [ + "465", + "UTHSCWGU88BFMEx1013", + "UTHSC WGU88 Male Bone Femur AFFY Mouse Gene ST 2.0 Exon Level (Oct13) RMA" + ], + [ + "466", + "UTHSCWGU88BFFG1013", + "UTHSC WGU88 Female Bone Femur AFFY Mouse Gene ST 2.0 Gene Level (Oct13) RMA" + ], + [ + "467", + "UTHSCWGU88BFFEx1013", + "UTHSC WGU88 Female Bone Femur AFFY Mouse Gene ST 2.0 Exon Level (Oct13) RMA" ] ], "Brain mRNA": [ @@ -2221,6 +2882,76 @@ "9", "CB_M_1003_M", "SJUT Cerebellum mRNA M430 (Oct03) MAS5" + ], + [ + "436", + "CMMTUBCBXDCerILM0513", + "UBC/CMMT BXD Cerebellum All Ages Combined ILM Mouse WG-6 v2.0 (May13) RankInv" + ], + [ + "441", + "CMMTUBCBXDG12CerILM0513", + "UBC/CMMT BXD E12 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv" + ], + [ + "442", + "CMMTUBCBXDG15CerILM0513", + "UBC/CMMT BXD E15 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv" + ], + [ + "443", + "CMMTUBCBXDG18CerILM0513", + "UBC/CMMT BXD E18 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv" + ], + [ + "437", + "CMMTUBCBXDP00CerILM0513", + "UBC/CMMT BXD P0 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv" + ], + [ + "438", + "CMMTUBCBXDP03CerILM0513", + "UBC/CMMT BXD P3 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv" + ], + [ + "439", + "CMMTUBCBXDP06CerILM0513", + "UBC/CMMT BXD P6 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv" + ], + [ + "440", + "CMMTUBCBXDP09CerILM0513", + "UBC/CMMT BXD P9 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv" + ], + [ + "415", + "GenEx_BXD_CerebEt_RMA_0213", + "GenEx BXD EtOH Cerebellum Affy M430 2.0 (Feb13) RMA Both Sexes" + ], + [ + "416", + "GenEx_BXD_CerebEt_RMA_F_0213", + "GenEx BXD EtOH Cerebellum Affy M430 2.0 (Feb13) RMA Females" + ], + [ + "417", + "GenEx_BXD_CerebEt_RMA_M_0213", + "GenEx BXD EtOH Cerebellum Affy M430 2.0 (Feb13) RMA Males" + ], + [ + "418", + "GenEx_BXD_CerebSal_RMA_0213", + "GenEx BXD Sal Cerebellum Affy M430 2.0 (Feb13) RMA Both Sexes" + ], + [ + "419", + "GenEx_BXD_CerebSal_RMA_F_0213", + "GenEx BXD Sal Cerebellum Affy M430 2.0 (Feb13) RMA Females" + ], + [ + "420", + "GenEx_BXD_CerebSal_RMA_M_0213", + "GenEx BXD Sal Cerebellum Affy M430 2.0 (Feb13) RMA Males" ] ], "Eye mRNA": [ @@ -2297,6 +3028,21 @@ "597", "UTHSC_GutExL_0414", "UTHSC Mouse BXD Gastrointestinal Affy MoGene 1.0 ST Exon Level (Apr14) RMA" + ], + [ + "839", + "EPFL-LISP_BXD_Col-CD+HFD0917", + "EPFL/LISP BXD CD+HFD Gastrointestinal Affy Clariom S GeneLevel Main (Sep17) RMA" + ], + [ + "841", + "EPFL-LISP_BXD_Col-HFD0917", + "EPFL/LISP BXD HFD Gastrointestinal Affy Clariom S GeneLevel Main (Sep17) RMA" + ], + [ + "840", + "EPFL-LISP_BXD_Col-CD0917", + "EPFL/LISP BXD CD Gastrointestinal Affy Clariom S GeneLevel Main (Sep17) RMA" ] ], "Genotypes": [ @@ -2502,6 +3248,23 @@ "711", "UTHSC_BXD_AgeHipp0515", "UTHSC BXD Aged Hippocampus Affy MoGene1.0 ST (May15) RMA Gene Level" + ], + [ + "393", + "UTHSC_BXD_HArev3_0912", + "UTHSC BXD Aged Hippocampus rev3 Affy Mouse Gene 1.0 ST (Sep12) RMA" + ], + [ + "392", + "UTHSC_BXD_H_0912", + "UTHSC BXD Aged Hippocampus Affy Mouse Gene 1.0 ST (Sep12) RMA Exon Level" + ] + ], + "Hippocampus microRNA": [ + [ + "491", + "UTHSC_BXD_Hip_miRNASeq0214", + "UTHSC BXD Hippocampus Ion Torrent microRNA (Feb14) RPKM*" ] ], "Hypothalamus mRNA": [ @@ -2578,6 +3341,30 @@ "Mouse Kidney M430v2 (Jul06) PDNN" ] ], + "Leucocytes mRNA": [ + [ + "218", + "Illum_BXD_PBL_1108", + "UWA Illumina PBL (Nov08) RSN*" + ] + ], + "Liver DNAm": [ + [ + "891", + "UTHSC-BXD-LivDNAm-1119", + "UTHSC BXD Liver CD-HFD DNAm (Nov19) Sesame" + ], + [ + "892", + "UTHSC-BXD-LivHFDNAm-1119", + "UTHSC BXD Liver HFD DNAm (Nov19) Sesame" + ], + [ + "893", + "UTHSC-BXD-LivCDNAm-1119", + "UTHSC BXD Liver CD DNAm (Nov19) Sesame" + ] + ], "Liver Metabolome": [ [ "835", @@ -2616,6 +3403,21 @@ ] ], "Liver Proteome": [ + [ + "887", + "EPFL-ETHZ-BXD-LivProtAvg-CD-HF-1119", + "EPFL/ETHZ BXD Liver Proteome CD+HFD (Nov19)" + ], + [ + "888", + "EPFL-ETHZ-BXD-LivProtAvg-CD-1119", + "EPFL/ETHZ BXD Liver Proteome CD (Nov19)" + ], + [ + "889", + "EPFL-ETHZ-BXD-LivProtAvg-HFD-1119", + "EPFL/ETHZ BXD Liver Proteome HFD (Nov19)" + ], [ "540", "EPFLETHZBXDprotCD0514", @@ -2683,6 +3485,21 @@ "NIA-AgBXD-Liv_CD-rna-seq-0818", "NIA Aging BXD CD Liver RNA-Seq (Aug18) Log2" ], + [ + "851", + "NIA-AgBXD-Liv_CDHFD-0818", + "NIA Aging BXD CD+HFD Liver Affy Clariom S Gene Level (Aug18) RMA" + ], + [ + "852", + "NIA-AgBXD-Liv_HFD-0818", + "NIA Aging BXD HFD Liver Affy Clariom S Gene Level (Aug18) RMA" + ], + [ + "853", + "NIA-AgBXD-Liv_CD-0818", + "NIA Aging BXD CD Liver Affy Clariom S Gene Level (Aug18) RMA" + ], [ "818", "UCLA_BXD_Liv_Jan16", @@ -2799,6 +3616,26 @@ "161", "HZI_0408_M", "HZI Lung M430v2 (Apr08) MAS5" + ], + [ + "807", + "HZI_LungBXD_RNA-Seq_1116", + "HZI Lung Flu Infected BXD (Nov16) RNA-Seq*" + ], + [ + "598", + "HZI_PR8M-F_1014", + "HZI PR8M-Infected Lungs Females RNAseq (Oct14) RPKM Log2*" + ], + [ + "387", + "HZI_PR8M_Q_0612", + "HZI PR8M-Infected Lungs Agilent4x44 (Apr12) Quantile Females" + ], + [ + "424", + "HZI_LTCF_0313", + "HZI Lung Time Course Flu PR8M (Mar13) Schughart*" ] ], "Midbrain mRNA": [ @@ -2808,6 +3645,23 @@ "VU BXD Midbrain Agilent SurePrint G3 Mouse GE (May12) Quantile" ] ], + "Muscle Metabolome": [ + [ + "476", + "EPFL-LISP_MusPMetCDHFD1213", + "EPFL/LISP BXD Muscle Polar Metabolites CD+HFD (Jun14)" + ], + [ + "477", + "EPFL-LISP_MusPMetHFD1213", + "EPFL/LISP BXD Muscle Polar Metabolites HFD (Jun14)" + ], + [ + "478", + "EPFL-LISP_MusPMetCD1213", + "EPFL/LISP BXD Muscle Polar Metabolites CD (Jun14)" + ] + ], "Muscle mRNA": [ [ "378", @@ -2877,11 +3731,68 @@ "BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov10) RankInv" ] ], + "Neutrophils mRNA": [ + [ + "595", + "UTHSC-Neut-1014", + "UTHSC Elicited Peritoneal Neutrophils Affy MoGene 2.0 ST (Oct14) RMA" + ], + [ + "596", + "UTHSC-Neut_EL-1014", + "UTHSC Elicited Peritoneal Neutrophils Affy MoGene 2.0 ST (Oct14) RMA Exon Level" + ] + ], "Nucleus Accumbens mRNA": [ [ "156", "VCUSalo_1007_R", "VCU BXD NAc Sal M430 2.0 (Oct07) RMA" + ], + [ + "792", + "VCU_BXD_Nac_CIE_Air_0416", + "VCU BXD NAc CIE Air Masked ComBat M430 2.0 (Apr16) RMA" + ], + [ + "793", + "VCU_BXD_Nac_CIE_AirZ_0416", + "VCU BXD NAc CIE Air Masked ComBat M430 2.0 (Apr16) RMA Z-score" + ], + [ + "794", + "VCU_BXD_Nac_CIE_Et_0416", + "VCU BXD NAc CIE EtOH Masked ComBat M430 2.0 (Apr16) RMA" + ], + [ + "795", + "VCU_BXD_Nac_CIE_EtZ_0416", + "VCU BXD NAc CIE EtOH Masked ComBat M430 2.0 (Apr16) RMA Z-score" + ], + [ + "155", + "VCUEtOH_1007_R", + "VCU BXD NAc EtOH M430 2.0 (Oct07) RMA" + ], + [ + "154", + "VCUSal_1007_R", + "VCU BXD NAc EtOH vs Sal M430 2.0 (Oct07) Sscore*" + ], + [ + "409", + "VCU_NAc_Air_0113_R", + "VCU BXD NAc CIE Air M430 2.0 (Jan13) RMA" + ], + [ + "408", + "VCU_NAc_Et_0113_R", + "VCU BXD NAc CIE EtOH M430 2.0 (Jan13) RMA" + ], + [ + "407", + "VCU_NAc_AvE_0113_Ss", + "VCU BXD NAc EtOH vs CIE Air M430 2.0 (Jan13) Sscore*" ] ], "Phenotypes": [ @@ -2918,7 +3829,44 @@ "INIA Pituitary Affy MoGene 1.0ST (Jun12) RMA Exon Level" ] ], + "Popliteal Lymph Node mRNA": [ + [ + "390", + "STJ_PLN_0912", + "St Jude BXD Popliteal Lymph Node Affy HT MG-430 PM (Sep12) RMA" + ] + ], "Prefrontal Cortex mRNA": [ + [ + "898", + "DOD-BXD-PFC-CD-RNA-Seq-ComB-1019", + "DOD BXD PFC GWI CD RNA-Seq ComB (Dec19) TPM Log2" + ], + [ + "899", + "DOD-BXD-PFC-CTL-RNA-Seq-ComB-1019", + "DOD BXD PFC GWI CTL RNA-Seq ComB (Dec19) TPM Log2" + ], + [ + "900", + "DOD-BXD-PFC-DFP-RNA-Seq-ComB-1019", + "DOD BXD PFC GWI DFP RNA-Seq ComB (Dec19) TPM Log2" + ], + [ + "883", + "DOD-BXD-PFC-CD-RNA-Seq-1019", + "DOD BXD PFC GWI CD RNA-Seq (Oct19) TPM Log2" + ], + [ + "884", + "DOD-BXD-PFC-CTL-RNA-Seq-1019", + "DOD BXD PFC GWI CTL RNA-Seq (Oct19) TPM Log2" + ], + [ + "885", + "DOD-BXD-PFC-DFP-RNA-Seq-1019", + "DOD BXD PFC GWI DFP RNA-Seq (Oct19) TPM Log2" + ], [ "135", "VCUSal_1206_R", @@ -2933,6 +3881,41 @@ "137", "VCUSal_1006_R", "VCU BXD PFC Et vs Sal M430 2.0 (Dec06) Sscore" + ], + [ + "788", + "VCU_BXD_PFC_CIE_Air_0416", + "VCU BXD PFC CIE Air Masked ComBat M430 2.0 (Apr16) RMA" + ], + [ + "789", + "VCU_BXD_PFC_CIE_AirZ_0416", + "VCU BXD PFC CIE Air Masked ComBat M430 2.0 (Apr16) RMA Z-score" + ], + [ + "790", + "VCU_BXD_PFC_CIE_Et_0416", + "VCU BXD PFC CIE EtOH Masked ComBat M430 2.0 (Apr16) RMA" + ], + [ + "791", + "VCU_BXD_PFC_CIE_EtZ_0416", + "VCU BXD PFC CIE EtOH Masked ComBat M430 2.0 (Apr16) RMA Z-score" + ], + [ + "299", + "VCU_PF_AvE_0111_Ss", + "VCU BXD PFC EtOH vs CIE Air M430 2.0 (Jan11) Sscore*" + ], + [ + "300", + "VCU_PF_Et_0111_R", + "VCU BXD PFC CIE EtOH M430 2.0 (Jan11) RMA" + ], + [ + "301", + "VCU_PF_Air_0111_R", + "VCU BXD PFC CIE Air M430 2.0 (Jan11) RMA" ] ], "Retina mRNA": [ @@ -2971,11 +3954,26 @@ "DoDTATRCRetBLMoGene2E_0316", "DoD Retina After Blast Affy MoGene 2.0 ST (Mar16) RMA Exon Level" ], + [ + "796", + "DoDRetBlastvsNormalEx_0416", + "DoD Retina Blast vs Normal Retina Affy MoGene 2.0 ST (Apr16) RMA Exon Level" + ], [ "385", "ONCRetILM6_0412", "ONC HEI Retina (April 2012) RankInv" ], + [ + "386", + "B6D2ONCILM_0412", + "B6D2 ONC Retina (April 2012) RankInv" + ], + [ + "372", + "G2HEIONCRetILM6_0911", + "G2 HEI ONC Retina Illumina V6.2 (Sep11) RankInv" + ], [ "371", "HEIONCvsCRetILM6_0911", @@ -3027,6 +4025,11 @@ "227", "IoP_SPL_RMA_0509", "IoP Affy MOE 430v2 Spleen (May09) RMA" + ], + [ + "216", + "Illum_BXD_Spl_1108", + "UWA Illumina Spleen (Nov08) RSN*" ] ], "Striatum mRNA": [ @@ -3105,6 +4108,13 @@ "HZI Treg M430v2 (Feb11) RMA" ] ], + "Thymus mRNA": [ + [ + "217", + "Illum_BXD_Thy_1108", + "UWA Illumina Thymus (Nov08) RSN*" + ] + ], "Ventral Tegmental Area mRNA": [ [ "228", @@ -3140,28 +4150,52 @@ "BXD-Harvested Genotypes" ] ], - "Hippocampus mRNA": [ + "Hippocampus Proteome": [ [ "873", "JAX-BXD-Hip-Pro-0219", "JAX BXD Hippocampal Proteome (Feb19)" ] ], + "Liver DNAm": [ + [ + "890", + "INIA-BXD-LivDNAm-1119", + "INIA BXD Liver DNAm CD-HFD (Nov19) Sesame" + ] + ], + "Liver Proteome": [ + [ + "886", + "EPFL-ETHZ-BXD-LivProtCD-HF-1119", + "EPFL/ETHZ BXD Liver Proteome CD-HFD (Nov19)" + ] + ], "Liver mRNA": [ [ "877", "UTHSC-BXD-Harv_Liv-1019", "UTHSC BXD Harvested Liver RNA-Seq (Oct19) TPM Log2" ], + [ + "850", + "UTHSC-BXD-Liv-0818", + "UTHSC BXD Liver Affy Clariom S GeneLevel Main (Aug18) RMA" + ], [ "843", "UTHSC-BXD-Harv_Liv-0118", "UTHSC BXD Harvested Liver RNA-Seq (Aug18) Log2" + ], + [ + "842", + "UTHSC-BXD-Liv-0917", + "UTHSC BXD Liver Affy Clariom S GeneLevel Main (Sep17) RMA" ] ], "Phenotypes": [ [ - "None", + "660", "BXD-HarvestedPublish", "BXD-NIA-Longevity Phenotypes" ] @@ -3263,6 +4297,29 @@ ] ] }, + "CC": { + "Genotypes": [ + [ + "663", + "CCGeno", + "CC Genotypes" + ] + ], + "Midbrain mRNA": [ + [ + "894", + "LSRU-CC-ST-1219", + "LSRU CC Male Midbrain RNA-Seq (Dec19) TPM Log2" + ] + ], + "Phenotypes": [ + [ + "662", + "CCPublish", + "CC Phenotypes" + ] + ] + }, "CFW": { "Hippocampus mRNA": [ [ @@ -3360,9 +4417,35 @@ "CIE-RMAPublish", "CIE-RMA Phenotypes" ] + ], + "Prefrontal Cortex mRNA": [ + [ + "832", + "INIA_UTHSC_PFC_AffyMTA1_May17", + "INIA-UTHSC Prefrontal Cortex CIE Affy MTA 1.0 GeneLevel (Apr17) RMA" + ] + ], + "Striatum mRNA": [ + [ + "833", + "INIA_UTHSC_Str_AffyMTA1_May17", + "INIA-UTHSC Striatum CIE Affy MTA 1.0 GeneLevel (Apr17) RMA" + ] ] }, "CMS": { + "Hippocampus mRNA": [ + [ + "771", + "CMS_Hipp1115", + "Hippocampus Mouse Transcriptome Assay 1.0 Gene Level Main (Nov15) RMA" + ], + [ + "800", + "CMS_Hipp_ZScr_1115", + "Hippocampus Mouse Transcriptome Assay 1.0 Gene Level Z-Score (Nov15) RMA" + ] + ], "Phenotypes": [ [ "None", @@ -3520,6 +4603,92 @@ ] ] }, + "DOD-BXD-GWI": { + "Genotypes": [ + [ + "None", + "DOD-BXD-GWIGeno", + "DOD-BXD-GWI Genotypes" + ] + ], + "Prefrontal Cortex mRNA": [ + [ + "895", + "DOD-BXD-Ind-PFC-CD-RNA-Seq-ComB-1019", + "DOD BXD INDV PFC GWI CD RNA-Seq ComB (Dec19) TPM Log2" + ], + [ + "896", + "DOD-BXD-Ind-PFC-CTL-RNA-Seq-ComB-1019", + "DOD BXD INDV PFC GWI CTL RNA-Seq ComB (Dec19) TPM Log2" + ], + [ + "897", + "DOD-BXD-Ind-PFC-DFP-RNA-Seq-ComB-1019", + "DOD BXD INDV PFC GWI DFP RNA-Seq ComB (Dec19) TPM Log2" + ], + [ + "880", + "DOD-BXD-Ind-PFC-CD-RNA-Seq-1019", + "DOD BXD INDV PFC GWI CD RNA-Seq (Oct19) TPM Log2" + ], + [ + "881", + "DOD-BXD-Ind-PFC-CTL-RNA-Seq-1019", + "DOD BXD INDV PFC GWI CTL RNA-Seq (Oct19) TPM Log2" + ], + [ + "882", + "DOD-BXD-Ind-PFC-DFP-RNA-Seq-1019", + "DOD BXD INDV PFC GWI DFP RNA-Seq (Oct19) TPM Log2" + ] + ] + }, + "EMSR": { + "Hippocampus mRNA": [ + [ + "825", + "UTHSC_EMSR_All_AffyMTA1_Mar17", + "UTHSC Hippocampus All Treatments Affy MTA 1.0 Gene Level (Mar17) RMA" + ], + [ + "826", + "UTHSC_EMSR_Sal_AffyMTA1_Mar17", + "UTHSC Hippocampus Saline Affy MTA 1.0 Gene Level (Mar17) RMA" + ], + [ + "827", + "UTHSC_EMSR_Et_AffyMTA1_Mar17", + "UTHSC Hippocampus Ethanol Affy MTA 1.0 Gene Level (Mar17) RMA" + ], + [ + "828", + "UTHSC_EMSR_St_AffyMTA1_Mar17", + "UTHSC Hippocampus Stress Affy MTA 1.0 Gene Level (Mar17) RMA" + ], + [ + "829", + "UTHSC_EMSR_EtSt_AffyMTA1_Mar17", + "UTHSC Hippocampus Ethanol-Stress Affy MTA 1.0 Gene Level (Mar17) RMA" + ] + ] + }, + "HET3-ITP": { + "Genotypes": [ + [ + "None", + "HET3-ITPGeno", + "HET3-ITP Genotypes" + ] + ], + "Phenotypes": [ + [ + "661", + "HET3-ITPPublish", + "HET3 ITP Longevity Phenotypes" + ] + ] + }, "HS": { "Hippocampus mRNA": [ [ @@ -3559,16 +4728,123 @@ ] ] }, - "LGSM-AIG34_50-56-GBS": { + "JAX-D2-Mono-RNA-Seq": { + "Retina mRNA": [ + [ + "878", + "JAX-D2-Mono1vPBMC-Ret-RNA-Seq-0619", + "JAX DBA/2J Monocyte 1 vs PBMC RNA-Seq (Jun19)" + ], + [ + "879", + "JAX-D2-Mono2vPBMC-Ret-RNA-Seq-0619", + "JAX DBA/2J Monocyte 2 vs PBMC RNA-Seq (Jun19)" + ] + ] + }, + "LGSM-AI": { + "Hippocampus mRNA": [ + [ + "874", + "UCSD_AIL_HIP_RNA-Seq_log2_0418", + "UCSD AIL Hippocampus (Apr18) RNA-Seq Log2" + ], + [ + "844", + "UCSD_AIL_HIP_RNA-Seq_0418", + "UCSD AIL Hippocampus (Apr18) RNA-Seq" + ] + ], "Phenotypes": [ [ "None", + "LGSM-AIPublish", + "LGSM AI Phenotypes" + ] + ], + "Prefrontal Cortex mRNA": [ + [ + "876", + "UCSD_AIL_PFC_RNA-Seq_log2_0418", + "UCSD AIL Prefrontal Cortex (Apr18) RNA-Seq Log2" + ], + [ + "846", + "UCSD_AIL_PFC_RNA-Seq_0418", + "UCSD AIL Prefrontal Cortex (Apr18) RNA-Seq" + ] + ], + "Striatum mRNA": [ + [ + "875", + "UCSD_AIL_STR_RNA-Seq_log2_0418", + "UCSD AIL Striatum (Apr18) RNA-Seq Log2" + ], + [ + "845", + "UCSD_AIL_STR_RNA-Seq_0418", + "UCSD AIL Striatum (Apr18) RNA-Seq" + ] + ] + }, + "LGSM-AI-G34-A": { + "Phenotypes": [ + [ + "655", + "LGSM-AI-G34-APublish", + "LGSM AI G34 Phenotypes" + ] + ] + }, + "LGSM-AI-G34-GBS": { + "Phenotypes": [ + [ + "656", + "LGSM-AI-G34-GBSPublish", + "LGSM AI G34 GBS Phenotypes" + ] + ] + }, + "LGSM-AI-G34_39-43-GBS": { + "Phenotypes": [ + [ + "657", + "LGSM-AI-G34_39-43-GBSPublish", + "LGSM AI G34 G39-43 GBS Phenotypes" + ] + ] + }, + "LGSM-AI-G39-43-GBS": { + "Phenotypes": [ + [ + "654", + "LGSM-AI-G39-43-GBSPublish", + "LGSM AI G39-43 GBS Phenotypes" + ] + ] + }, + "LGSM-AIG34_50-56-GBS": { + "Phenotypes": [ + [ + "659", "LGSM-AIG34_50-56-GBSPublish", - "LGSM AIG34/50-56 GBS Phenotypes" + "LGSM AI G34/50-56 GBS Phenotypes" ] ] }, "LXS": { + "Brain mRNA": [ + [ + "783", + "UCAMC_LXSBrEtOH_RNA-Seq_0216", + "UCAMC LXS Whole Brain Ethanol RNA Sequence (Feb16) FPKM*" + ], + [ + "784", + "UCAMC_LXSBrSal_RNA-Seq_0216", + "UCAMC LXS Whole Brain Saline RNA Sequence (Feb16) FPKM*" + ] + ], "Genotypes": [ [ "601", @@ -3650,6 +4926,16 @@ "130", "VCUSal_0806_R", "VCU LXS PFC Sal M430A 2.0 (Aug06) RMA" + ], + [ + "132", + "VCUEt_vs_Sal_0806_R", + "VCU LXS PFC Et vs Sal M430A 2.0 (Aug06) Sscore*" + ], + [ + "131", + "VCUEtOH_0806_R", + "VCU LXS PFC EtOH M430A 2.0 (Aug06) RMA" ] ] }, @@ -3701,6 +4987,11 @@ "273", "UMUTAffyExon_0209_RMA_MDP", "UMUTAffy Hippocampus Exon (Feb09) RMA MDP" + ], + [ + "594", + "UFL-MDP-Hipp0814", + "UFL MDP Hippocampus Antidepressant Affy Mouse 430 2.0 (Aug14) RMA" ] ], "Liver mRNA": [ @@ -3795,6 +5086,36 @@ "SOTNOT-OHSU Genotypes" ] ] + }, + "Scripps-2013": { + "Anterior Cingulate Cortex mRNA": [ + [ + "450", + "ScrBXDACC4G0513", + "Scripps BXD ACC 4 Groups Affy Mouse Gene 1.0 ST (May13) RMA Gene Level" + ], + [ + "451", + "ScrBXDACC4GEx0513", + "Scripps BXD ACC 4 Groups Affy Mouse Gene 1.0 ST (May13) RMA Exon Level" + ] + ] + }, + "UTHSC-Cannabinoid": { + "Genotypes": [ + [ + "None", + "UTHSC-CannabinoidGeno", + "UTHSC-Cannabinoid Genotypes" + ] + ], + "Phenotypes": [ + [ + "None", + "UTHSC-CannabinoidPublish", + "UTHSC Cannabinoid Pilot Phenotypes" + ] + ] } }, "poplar": { @@ -3809,22 +5130,6 @@ } }, "rat": { - "HRDP": { - "Genotypes": [ - [ - "None", - "HRDPGeno", - "HRDP Genotypes" - ] - ], - "Phenotypes": [ - [ - "None", - "HRDPPublish", - "HRDP Phenotypes" - ] - ] - }, "HSNIH-Palmer": { "Infralimbic Cortex mRNA": [ [ @@ -4011,295 +5316,411 @@ "arabidopsis": [ [ "BayXSha", - "BayXSha" + "BayXSha", + "Family:None" ], [ "ColXBur", - "ColXBur" + "ColXBur", + "Family:None" ], [ "ColXCvi", - "ColXCvi" + "ColXCvi", + "Family:None" ] ], "barley": [ [ "QSM", - "QSM" + "QSM", + "Family:None" ], [ "SXM", - "SXM" + "SXM", + "Family:None" ] ], "drosophila": [ [ "DGRP", - "Drosophila Genetic Reference Panel" + "Drosophila Genetic Reference Panel", + "Family:None" ], [ "Oregon-R_x_2b3", - "Oregon-R x 2b3" + "Oregon-R x 2b3", + "Family:None" ] ], "human": [ [ "HB", - "Brain, Aging: AD, HD, Normal Gene Expression (Harvard/Merck)" + "Brain, Aging: AD, HD, Normal Gene Expression (Harvard/Merck)", + "Family:None" ], [ "AD-cases-controls", - "Brain, Aging: AD, Normal Gene Expression (Liang)" + "Brain, Aging: AD, Normal Gene Expression (Liang)", + "Family:None" ], [ "AD-cases-controls-Myers", - "Brain, Aging: AD, Normal Gene Expression with Genotypes (Myers)" + "Brain, Aging: AD, Normal Gene Expression with Genotypes (Myers)", + "Family:None" ], [ "Aging-Brain-UCI", - "Brain, Aging: Normal Gene Expression (UCI/Cotman)" + "Brain, Aging: Normal Gene Expression (UCI/Cotman)", + "Family:None" ], [ "HCP", - "Brain, Cognition, Human Connectome Project" + "Brain, Cognition, Human Connectome Project", + "Family:None" ], [ "HSB", - "Brain, Development: Normal Gene Expression (Yale/Sestan)" + "Brain, Development: Normal Gene Expression (Yale/Sestan)", + "Family:None" ], [ "Brain-Normal-NIH-Gibbs", - "Brain: Normal Gene Expression (NIH/Gibbs)" + "Brain: Normal Gene Expression (NIH/Gibbs)", + "Family:None" ], [ "CANDLE", - "Child Development: CANDLE Cohort with Genotypes (TUCI/UTHSC)" + "Child Development: CANDLE Cohort with Genotypes (TUCI/UTHSC)", + "Family:None" ], [ "GTEx", - "GTEx v3 All Tissues, RNA-Seq with Genotypes" + "GTEx v3 All Tissues, RNA-Seq with Genotypes", + "Family:None" ], [ "GTEx_v5", - "GTEx v5 All Tissues, RNA-Seq with Genotypes" + "GTEx v5 All Tissues, RNA-Seq with Genotypes", + "Family:None" + ], + [ + "GTEx_v8", + "GTEx v8 All Tissues, RNA-Seq without Genotypes", + "Family:None" ], [ "HLC", - "Liver: Normal Gene Expression with Genotypes (Merck)" + "Liver: Normal Gene Expression with Genotypes (Merck)", + "Family:None" ], [ "HLT", - "Lung: Normal Gene Expression (Merck)" + "Lung: Normal Gene Expression (Merck)", + "Family:None" ], [ "CEPH-2004", - "Lymphoblastoid Cells: Gene Expression (CEPH, Williams)" + "Lymphoblastoid Cells: Gene Expression (CEPH, Williams)", + "Family:None" ], [ "Islets-Gerling", - "Pancreatic: Islets (UTHSC/Gerling)" + "Pancreatic: Islets (UTHSC/Gerling)", + "Family:None" ], [ "TIGEM-Retina-RNA-Seq", - "Retina: Normal Adult Gene Expression, RNA-Seq (TIGEM)" + "Retina: Normal Adult Gene Expression, RNA-Seq (TIGEM)", + "Family:None" + ] + ], + "macaque monkey": [ + [ + "Macaca-fasicularis", + "Macaca fasicularis (Cynomolgus monkey)", + "Family:None" ] ], "mouse": [ [ - "AIL", - "AIL Advanced Intercross Line" + "AKXD", + "AKXD Family", + "Family:Reference Populations" + ], + [ + "AXBXA", + "AXB/BXA Family", + "Family:Reference Populations" + ], + [ + "BXD", + "BXD Family", + "Family:Reference Populations" + ], + [ + "BXH", + "BXH Family", + "Family:Reference Populations" + ], + [ + "CC", + "CC Family", + "Family:Reference Populations" + ], + [ + "CXB", + "CXB Family", + "Family:Reference Populations" + ], + [ + "LXS", + "ILSXISS (LXS) Family", + "Family:Reference Populations" + ], + [ + "MDP", + "Mouse Diversity Panel", + "Family:Reference Populations" + ], + [ + "B6D2RI", + "BXD Aged Hippocampus", + "Family:BXD Individual Data" ], [ - "AIL-LGSM-F34-A", - "AIL LGSM F34 (Array)" + "BXD-Bone", + "BXD Bone Individual Data", + "Family:BXD Individual Data" ], [ - "AIL-LGSM-F34-GBS", - "AIL LGSM F34 (GBS)" + "DOD-BXD-GWI", + "BXD DOD Gulf War Illness", + "Family:BXD Individual Data" ], [ - "AIL-LGSM-F34-F39-43-GBS", - "AIL LGSM F34 and F39-43 (GBS)" + "BXD-Harvested", + "BXD NIA Longevity Study", + "Family:BXD Individual Data" ], [ - "AIL-LGSM-F39-43-GBS", - "AIL LGSM F39-43 (GBS)" + "UTHSC-Cannabinoid", + "BXD UTHSC Cannabinoid Pilot", + "Family:BXD Individual Data" ], [ - "AKXD", - "AKXD RI Family" + "B6BTBRF2", + "B6BTBRF2", + "Family:Crosses, AIL, HS" ], [ - "AXBXA", - "AXB/BXA RI Family" + "BHHBF2", + "B6C3HF2 UCLA Metabolism", + "Family:Crosses, AIL, HS" ], [ - "B6BTBRF2", - "B6BTBRF2" + "BHF2", + "B6C3HF2(APOE-) UCLA Metabolism", + "Family:Crosses, AIL, HS" ], [ "Linsenbardt-Boehm", - "B6D2 EtOH Selected Advanced Intercross" + "B6D2 EtOH Selected Advanced Intercross", + "Family:Crosses, AIL, HS" ], [ "B6D2F2", - "B6D2F2" - ], - [ - "B6D2F2-PSU", - "B6D2F2 PSU" + "B6D2F2 OHSU Brain", + "Family:Crosses, AIL, HS" ], [ - "BDF2-1999", - "BDF2 UCLA" + "BDF2-2005", + "B6D2F2 OHSU Striatum", + "Family:Crosses, AIL, HS" ], [ - "BDF2-2005", - "BDF2-2005" + "B6D2F2-PSU", + "B6D2F2 PSU Muscle", + "Family:Crosses, AIL, HS" ], [ - "BHHBF2", - "BH/HB F2 UCLA" + "BDF2-1999", + "B6D2F2 UCLA Liver", + "Family:Crosses, AIL, HS" ], [ - "BHF2", - "BHF2 (Apoe Null) UCLA" + "CTB6F2", + "CastB6/B6Cast F2 UCLA", + "Family:Crosses, AIL, HS" ], [ - "B6D2RI", - "BXD Aged" + "CFW", + "CFW Outbred GWAS", + "Family:Crosses, AIL, HS" ], [ - "BXD-Bone", - "BXD Bone Individual Data" + "HET3-ITP", + "HET3 ITP Longevity", + "Family:Crosses, AIL, HS" ], [ - "BXD-Harvested", - "BXD NIA Longevity Study" + "HS", + "Heterogeneous Stock", + "Family:Crosses, AIL, HS" ], [ - "BXD", - "BXD RI Family" + "HS-CC", + "Heterogeneous Stock Collaborative Cross", + "Family:Crosses, AIL, HS" ], [ - "BXD300", - "BXD300" + "LGSM-AI-G34_39-43-GBS", + "LGSM AI G34 G39-43 Palmer (GBS)", + "Family:Crosses, AIL, HS" ], [ - "BXH", - "BXH RI Family" + "LGSM-AI-G34-A", + "LGSM AI G34 Palmer (Array)", + "Family:Crosses, AIL, HS" ], [ - "CTB6F2", - "CastB6/B6Cast F2 UCLA" + "LGSM-AI-G34-GBS", + "LGSM AI G34 Palmer (GBS)", + "Family:Crosses, AIL, HS" ], [ - "CFW", - "CFW Outbred GWAS" + "LGSM-AIG34_50-56-GBS", + "LGSM AI G34/50-56 Lionikas (GBS)", + "Family:Crosses, AIL, HS" ], [ - "CIE-INIA", - "Chronic Intermittent Ethanol Phase 1" + "LGSM-AI-G39-43-GBS", + "LGSM AI G39-43 Palmer (GBS)", + "Family:Crosses, AIL, HS" ], [ - "CIE-RMA", - "Chronic Intermittent Ethanol Phase 2" + "LGSM-AI", + "LGSM AI Palmer", + "Family:Crosses, AIL, HS" ], [ - "CMS", - "Chronic Mild Stress" + "SOTNOT-OHSU", + "SOTNOT-OHSU", + "Family:Crosses, AIL, HS" ], [ - "CXB", - "CXB RI Family (strain means)" + "B6-Lens", + "B6 Lens", + "Family:Non-genetic Cohort" ], [ - "D2GM", - "D2 Glaucoma Model" + "CIE-INIA", + "Chronic Intermittent Ethanol Phase 1", + "Family:Non-genetic Cohort" ], [ - "B6D2", - "Glaucoma and Aged Retina, UTHSC" + "CIE-RMA", + "Chronic Intermittent Ethanol Phase 2", + "Family:Non-genetic Cohort" ], [ - "HS", - "Heterogeneous Stock" + "CMS", + "Chronic Mild Stress", + "Family:Non-genetic Cohort" ], [ - "HS-CC", - "Heterogeneous Stock Collaborative Cross" + "D2GM", + "D2 Glaucoma Model", + "Family:Non-genetic Cohort" ], [ - "LXS", - "ILSXISS (LXS) RI Family (strain means)" + "JAX-D2-Mono-RNA-Seq", + "D2 Glaucoma Monocyte JAX", + "Family:Non-genetic Cohort" ], [ - "LGSM-AIG34_50-56-GBS", - "LGSM AI G34/50-56 Lionikas (GBS)" + "EMSR", + "Ethanol-Medicated Stress Reduction", + "Family:Non-genetic Cohort" ], [ - "MDP", - "Mouse Diversity Panel (strain means)" + "B6D2", + "Glaucoma and Aged Retina UTHSC", + "Family:Non-genetic Cohort" ], [ "NZBXFVB-N2", - "NZB/FVB N2 NCI" + "NZB/FVB N2 NCI", + "Family:Non-genetic Cohort" ], [ "C57BL-6JxC57BL-6NJF2", - "Reduced Complexity Cross (B6JxB6N F2)" + "Reduced Complexity Cross (B6JxB6N F2)", + "Family:Non-genetic Cohort" ], [ "Retina-RGC-Rheaume", - "Retina RGC Rheaume" + "Retina RGC Rheaume", + "Family:Non-genetic Cohort" ], [ - "SOTNOT-OHSU", - "SOTNOT-OHSU" + "Scripps-2013", + "Scripps C57BL/6J", + "Family:Non-genetic Cohort" + ], + [ + "BXD300", + "BXD300", + "Family:None" ] ], "poplar": [ [ "Poplar", - "Poplar" + "Poplar", + "Family:None" ] ], "rat": [ [ "HXBBXH", - "HXB/BXH" - ], - [ - "HRDP", - "Hybrid Rat Diversity Panel" + "Hybrid Rat Diversity Panel (Includes HXB/BXH)", + "Family:None" ], [ "HSNIH-Palmer", - "NIH Heterogeneous Stock (Palmer)" + "NIH Heterogeneous Stock (Palmer)", + "Family:None" ], [ "HSNIH-RGSMC", - "NIH Heterogeneous Stock (RGSMC 2013)" + "NIH Heterogeneous Stock (RGSMC 2013)", + "Family:None" ], [ "SRxSHRSPF2", - "UIOWA SRxSHRSP F2" + "UIOWA SRxSHRSP F2", + "Family:None" ] ], "soybean": [ [ "J12XJ58F11", - "J12XJ58F11" + "J12XJ58F11", + "Family:None" ], [ "J12XJ58F2", - "J12XJ58F2" + "J12XJ58F2", + "Family:None" ] ], "tomato": [ [ "LXP", - "LXP" + "LXP", + "Family:None" ] ] }, @@ -4308,6 +5729,10 @@ "human", "Human (hg19)" ], + [ + "macaque monkey", + "Macaque monkey" + ], [ "mouse", "Mouse (mm10)" @@ -4480,6 +5905,10 @@ "Phenotypes", "Phenotypes" ], + [ + "Methylation", + "Methylation" + ], [ "Newborn Cord Blood mRNA", "Newborn Cord Blood mRNA" @@ -4493,12 +5922,206 @@ ], "GTEx": [ [ - "Adipose tissue, subcutaneous mRNA", - "Adipose tissue, subcutaneous mRNA" + "Adipose Tissue, Subcutaneous mRNA", + "Adipose Tissue, Subcutaneous mRNA" + ], + [ + "Adipose Tissue, Visceral mRNA", + "Adipose Tissue, Visceral mRNA" + ], + [ + "Adrenal Gland mRNA", + "Adrenal Gland mRNA" + ], + [ + "Amygdala mRNA", + "Amygdala mRNA" + ], + [ + "Anterior Cingulate Cortex mRNA", + "Anterior Cingulate Cortex mRNA" + ], + [ + "Aorta mRNA", + "Aorta mRNA" + ], + [ + "Blood, Cells - EBV-Transformed Lymphocytes mRNA", + "Blood, Cells - EBV-Transformed Lymphocytes mRNA" + ], + [ + "Breast - Mammary Tissue mRNA", + "Breast - Mammary Tissue mRNA" + ], + [ + "Caudate mRNA", + "Caudate mRNA" + ], + [ + "Cells - EBV-Transformed Lymphocytes mRNA", + "Cells - EBV-Transformed Lymphocytes mRNA" + ], + [ + "Cells - Leukemia Cell Line (CML) mRNA", + "Cells - Leukemia Cell Line (CML) mRNA" + ], + [ + "Cells - Transformed Fibroblasts mRNA", + "Cells - Transformed Fibroblasts mRNA" + ], + [ + "Cerebellar Cortex mRNA", + "Cerebellar Cortex mRNA" + ], + [ + "Cerebellar Hemisphere mRNA", + "Cerebellar Hemisphere mRNA" + ], + [ + "Cerebellum mRNA", + "Cerebellum mRNA" + ], + [ + "Colon - Transverse mRNA", + "Colon - Transverse mRNA" + ], + [ + "Coronary mRNA", + "Coronary mRNA" + ], + [ + "Esophagus - Mucosa mRNA", + "Esophagus - Mucosa mRNA" + ], + [ + "Esophagus - Muscularis mRNA", + "Esophagus - Muscularis mRNA" + ], + [ + "Fallopian Tube mRNA", + "Fallopian Tube mRNA" + ], + [ + "Frontal Cortex mRNA", + "Frontal Cortex mRNA" + ], + [ + "Heart - Atrial Appendage mRNA", + "Heart - Atrial Appendage mRNA" + ], + [ + "Heart - Left Ventricle mRNA", + "Heart - Left Ventricle mRNA" + ], + [ + "Hippocampus mRNA", + "Hippocampus mRNA" + ], + [ + "Hypothalamus mRNA", + "Hypothalamus mRNA" + ], + [ + "Kidney mRNA", + "Kidney mRNA" + ], + [ + "Liver mRNA", + "Liver mRNA" + ], + [ + "Lung mRNA", + "Lung mRNA" + ], + [ + "Muscle mRNA", + "Muscle mRNA" + ], + [ + "Nerve - Tibial mRNA", + "Nerve - Tibial mRNA" + ], + [ + "Nucleus Accumbens mRNA", + "Nucleus Accumbens mRNA" + ], + [ + "Ovary mRNA", + "Ovary mRNA" + ], + [ + "Pancreas mRNA", + "Pancreas mRNA" + ], + [ + "Pituitary Gland mRNA", + "Pituitary Gland mRNA" + ], + [ + "Prostate mRNA", + "Prostate mRNA" + ], + [ + "Putamen mRNA", + "Putamen mRNA" + ], + [ + "Skin - Not Sun Exposed (Suprapubic) mRNA", + "Skin - Not Sun Exposed (Suprapubic) mRNA" + ], + [ + "Skin - Sun Exposed (Lower leg) mRNA", + "Skin - Sun Exposed (Lower leg) mRNA" + ], + [ + "Spinal Cord mRNA", + "Spinal Cord mRNA" + ], + [ + "Stomach mRNA", + "Stomach mRNA" + ], + [ + "Substantia Nigra mRNA", + "Substantia Nigra mRNA" + ], + [ + "Testis mRNA", + "Testis mRNA" + ], + [ + "Thyroid mRNA", + "Thyroid mRNA" + ], + [ + "Tibial mRNA", + "Tibial mRNA" + ], + [ + "Uterus mRNA", + "Uterus mRNA" + ], + [ + "Vagina mRNA", + "Vagina mRNA" + ], + [ + "Whole Blood mRNA", + "Whole Blood mRNA" + ] + ], + "GTEx_v5": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Adipose Tissue, Subcutaneous mRNA", + "Adipose Tissue, Subcutaneous mRNA" ], [ - "Adipose tissue, visceral mRNA", - "Adipose tissue, visceral mRNA" + "Adipose Tissue, Visceral mRNA", + "Adipose Tissue, Visceral mRNA" ], [ "Adrenal Gland mRNA", @@ -4517,8 +6140,12 @@ "Aorta mRNA" ], [ - "Blood, Cells - EBV-Transformed Lymphocytes mRNA", - "Blood, Cells - EBV-Transformed Lymphocytes mRNA" + "Bladder mRNA", + "Bladder mRNA" + ], + [ + "Bone Marrow mRNA", + "Bone Marrow mRNA" ], [ "Breast - Mammary Tissue mRNA", @@ -4532,10 +6159,6 @@ "Cells - EBV-Transformed Lymphocytes mRNA", "Cells - EBV-Transformed Lymphocytes mRNA" ], - [ - "Cells - Leukemia Cell Line (CML) mRNA", - "Cells - Leukemia Cell Line (CML) mRNA" - ], [ "Cells - Transformed Fibroblasts mRNA", "Cells - Transformed Fibroblasts mRNA" @@ -4552,6 +6175,14 @@ "Cerebellum mRNA", "Cerebellum mRNA" ], + [ + "Cervix mRNA", + "Cervix mRNA" + ], + [ + "Colon - Sigmoid mRNA", + "Colon - Sigmoid mRNA" + ], [ "Colon - Transverse mRNA", "Colon - Transverse mRNA" @@ -4560,6 +6191,10 @@ "Coronary mRNA", "Coronary mRNA" ], + [ + "Esophagus - Gastroesophageal mRNA", + "Esophagus - Gastroesophageal mRNA" + ], [ "Esophagus - Mucosa mRNA", "Esophagus - Mucosa mRNA" @@ -4636,6 +6271,10 @@ "Putamen mRNA", "Putamen mRNA" ], + [ + "Salivary Gland mRNA", + "Salivary Gland mRNA" + ], [ "Skin - Not Sun Exposed (Suprapubic) mRNA", "Skin - Not Sun Exposed (Suprapubic) mRNA" @@ -4644,10 +6283,18 @@ "Skin - Sun Exposed (Lower leg) mRNA", "Skin - Sun Exposed (Lower leg) mRNA" ], + [ + "Small Intestine - Terminal Ileum mRNA", + "Small Intestine - Terminal Ileum mRNA" + ], [ "Spinal Cord mRNA", "Spinal Cord mRNA" ], + [ + "Spleen mRNA", + "Spleen mRNA" + ], [ "Stomach mRNA", "Stomach mRNA" @@ -4681,18 +6328,18 @@ "Whole Blood mRNA" ] ], - "GTEx_v5": [ + "GTEx_v8": [ [ "Phenotypes", "Phenotypes" ], [ - "Adipose tissue, subcutaneous mRNA", - "Adipose tissue, subcutaneous mRNA" + "Adipose Tissue, Subcutaneous mRNA", + "Adipose Tissue, Subcutaneous mRNA" ], [ - "Adipose tissue, visceral mRNA", - "Adipose tissue, visceral mRNA" + "Adipose Tissue, Visceral mRNA", + "Adipose Tissue, Visceral mRNA" ], [ "Adrenal Gland mRNA", @@ -4710,14 +6357,6 @@ "Aorta mRNA", "Aorta mRNA" ], - [ - "Bladder mRNA", - "Bladder mRNA" - ], - [ - "Bone Marrow mRNA", - "Bone Marrow mRNA" - ], [ "Breast - Mammary Tissue mRNA", "Breast - Mammary Tissue mRNA" @@ -4746,10 +6385,6 @@ "Cerebellum mRNA", "Cerebellum mRNA" ], - [ - "Cervix mRNA", - "Cervix mRNA" - ], [ "Colon - Sigmoid mRNA", "Colon - Sigmoid mRNA" @@ -4774,10 +6409,6 @@ "Esophagus - Muscularis mRNA", "Esophagus - Muscularis mRNA" ], - [ - "Fallopian Tube mRNA", - "Fallopian Tube mRNA" - ], [ "Frontal Cortex mRNA", "Frontal Cortex mRNA" @@ -5009,6 +6640,10 @@ [ "Phenotypes", "Phenotypes" + ], + [ + "Islets mRNA", + "Islets mRNA" ] ], "TIGEM-Retina-RNA-Seq": [ @@ -5022,53 +6657,31 @@ ] ] }, - "mouse": { - "AIL": [ + "macaque monkey": { + "Macaca-fasicularis": [ [ - "Phenotypes", - "Phenotypes" + "Amygdala mRNA", + "Amygdala mRNA" ], [ - "Genotypes", - "Genotypes" + "Brain mRNA", + "Brain mRNA" ], [ "Hippocampus mRNA", "Hippocampus mRNA" ], [ - "Prefrontal Cortex mRNA", - "Prefrontal Cortex mRNA" + "Nucleus Accumbens mRNA", + "Nucleus Accumbens mRNA" ], [ - "Striatum mRNA", - "Striatum mRNA" - ] - ], - "AIL-LGSM-F34-A": [ - [ - "Phenotypes", - "Phenotypes" - ] - ], - "AIL-LGSM-F34-F39-43-GBS": [ - [ - "Phenotypes", - "Phenotypes" - ] - ], - "AIL-LGSM-F34-GBS": [ - [ - "Phenotypes", - "Phenotypes" - ] - ], - "AIL-LGSM-F39-43-GBS": [ - [ - "Phenotypes", - "Phenotypes" + "Prefrontal Cortex mRNA", + "Prefrontal Cortex mRNA" ] - ], + ] + }, + "mouse": { "AKXD": [ [ "Genotypes", @@ -5105,6 +6718,16 @@ "Liver mRNA" ] ], + "B6-Lens": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Ocular Lens mRNA", + "Ocular Lens mRNA" + ] + ], "B6BTBRF2": [ [ "Phenotypes", @@ -5123,6 +6746,14 @@ [ "Phenotypes", "Phenotypes" + ], + [ + "Retina microRNA", + "Retina microRNA" + ], + [ + "Retina mRNA", + "Retina mRNA" ] ], "B6D2F2": [ @@ -5143,6 +6774,10 @@ [ "Genotypes", "Genotypes" + ], + [ + "Muscle mRNA", + "Muscle mRNA" ] ], "B6D2RI": [ @@ -5195,6 +6830,10 @@ [ "Liver mRNA", "Liver mRNA" + ], + [ + "Muscle mRNA", + "Muscle mRNA" ] ], "BHHBF2": [ @@ -5284,6 +6923,10 @@ "Hippocampal Precursor Cells mRNA", "Hippocampal Precursor Cells mRNA" ], + [ + "Hippocampus microRNA", + "Hippocampus microRNA" + ], [ "Hippocampus mRNA", "Hippocampus mRNA" @@ -5296,6 +6939,14 @@ "Kidney mRNA", "Kidney mRNA" ], + [ + "Leucocytes mRNA", + "Leucocytes mRNA" + ], + [ + "Liver DNAm", + "Liver DNAm" + ], [ "Liver Metabolome", "Liver Metabolome" @@ -5316,6 +6967,10 @@ "Midbrain mRNA", "Midbrain mRNA" ], + [ + "Muscle Metabolome", + "Muscle Metabolome" + ], [ "Muscle mRNA", "Muscle mRNA" @@ -5324,6 +6979,10 @@ "Neocortex mRNA", "Neocortex mRNA" ], + [ + "Neutrophils mRNA", + "Neutrophils mRNA" + ], [ "Nucleus Accumbens mRNA", "Nucleus Accumbens mRNA" @@ -5332,6 +6991,10 @@ "Pituitary Gland mRNA", "Pituitary Gland mRNA" ], + [ + "Popliteal Lymph Node mRNA", + "Popliteal Lymph Node mRNA" + ], [ "Prefrontal Cortex mRNA", "Prefrontal Cortex mRNA" @@ -5356,6 +7019,10 @@ "T Cell (regulatory) mRNA", "T Cell (regulatory) mRNA" ], + [ + "Thymus mRNA", + "Thymus mRNA" + ], [ "Ventral Tegmental Area mRNA", "Ventral Tegmental Area mRNA" @@ -5377,12 +7044,20 @@ "Genotypes" ], [ - "Hippocampus mRNA", - "Hippocampus mRNA" + "Hippocampus Proteome", + "Hippocampus Proteome" + ], + [ + "Liver DNAm", + "Liver DNAm" ], [ "Liver mRNA", "Liver mRNA" + ], + [ + "Liver Proteome", + "Liver Proteome" ] ], "BXD300": [ @@ -5431,6 +7106,20 @@ "Genotypes" ] ], + "CC": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Genotypes", + "Genotypes" + ], + [ + "Midbrain mRNA", + "Midbrain mRNA" + ] + ], "CFW": [ [ "Phenotypes", @@ -5471,12 +7160,24 @@ [ "Midbrain mRNA", "Midbrain mRNA" + ], + [ + "Prefrontal Cortex mRNA", + "Prefrontal Cortex mRNA" + ], + [ + "Striatum mRNA", + "Striatum mRNA" ] ], "CMS": [ [ "Phenotypes", "Phenotypes" + ], + [ + "Hippocampus mRNA", + "Hippocampus mRNA" ] ], "CTB6F2": [ @@ -5541,6 +7242,32 @@ "Retina mRNA" ] ], + "DOD-BXD-GWI": [ + [ + "Genotypes", + "Genotypes" + ], + [ + "Prefrontal Cortex mRNA", + "Prefrontal Cortex mRNA" + ] + ], + "EMSR": [ + [ + "Hippocampus mRNA", + "Hippocampus mRNA" + ] + ], + "HET3-ITP": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Genotypes", + "Genotypes" + ] + ], "HS": [ [ "Phenotypes", @@ -5565,6 +7292,54 @@ "Striatum mRNA" ] ], + "JAX-D2-Mono-RNA-Seq": [ + [ + "Retina mRNA", + "Retina mRNA" + ] + ], + "LGSM-AI": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Hippocampus mRNA", + "Hippocampus mRNA" + ], + [ + "Prefrontal Cortex mRNA", + "Prefrontal Cortex mRNA" + ], + [ + "Striatum mRNA", + "Striatum mRNA" + ] + ], + "LGSM-AI-G34-A": [ + [ + "Phenotypes", + "Phenotypes" + ] + ], + "LGSM-AI-G34-GBS": [ + [ + "Phenotypes", + "Phenotypes" + ] + ], + "LGSM-AI-G34_39-43-GBS": [ + [ + "Phenotypes", + "Phenotypes" + ] + ], + "LGSM-AI-G39-43-GBS": [ + [ + "Phenotypes", + "Phenotypes" + ] + ], "LGSM-AIG34_50-56-GBS": [ [ "Phenotypes", @@ -5580,6 +7355,10 @@ "Genotypes", "Genotypes" ], + [ + "Brain mRNA", + "Brain mRNA" + ], [ "Hippocampus mRNA", "Hippocampus mRNA" @@ -5654,6 +7433,22 @@ "Genotypes", "Genotypes" ] + ], + "Scripps-2013": [ + [ + "Anterior Cingulate Cortex mRNA", + "Anterior Cingulate Cortex mRNA" + ] + ], + "UTHSC-Cannabinoid": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Genotypes", + "Genotypes" + ] ] }, "poplar": { @@ -5665,16 +7460,6 @@ ] }, "rat": { - "HRDP": [ - [ - "Phenotypes", - "Phenotypes" - ], - [ - "Genotypes", - "Genotypes" - ] - ], "HSNIH-Palmer": [ [ "Phenotypes", -- cgit v1.2.3 From 75ecdb25c7a598f0f254f4f53529b657736aaa49 Mon Sep 17 00:00:00 2001 From: zsloan Date: Mon, 27 Apr 2020 14:00:34 -0500 Subject: Made change that should allow dataset structure to be loaded from Redis instead of the JSON file without breaking things --- wqflask/base/data_set.py | 41 +++++++++++++--------- wqflask/wqflask/__init__.py | 4 +-- wqflask/wqflask/api/gen_menu.py | 18 ---------- wqflask/wqflask/collect.py | 2 +- .../new/javascript/dataset_select_menu_orig.js | 1 + 5 files changed, 28 insertions(+), 38 deletions(-) diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 1f99df49..fd1dff5c 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -93,22 +93,26 @@ Publish or ProbeSet. E.g. """ self.datasets = {} - data = json.loads(requests.get(GN2_BASE_URL + "/api/v_pre1/gen_dropdown").content) - #data = gen_menu.gen_dropdown_json() - - - for species in data['datasets']: - for group in data['datasets'][species]: - for dataset_type in data['datasets'][species][group]: - for dataset in data['datasets'][species][group][dataset_type]: - short_dataset_name = dataset[1] - if dataset_type == "Phenotypes": - new_type = "Publish" - elif dataset_type == "Genotypes": - new_type = "Geno" - else: - new_type = "ProbeSet" - self.datasets[short_dataset_name] = new_type + + data = Redis.get("dataset_structure") + if data: + self.datasets = json.loads(data) + else: #ZS: I don't think this should ever run unless Redis is emptied + data = json.loads(requests.get(GN2_BASE_URL + "/api/v_pre1/gen_dropdown").content) + for species in data['datasets']: + for group in data['datasets'][species]: + for dataset_type in data['datasets'][species][group]: + for dataset in data['datasets'][species][group][dataset_type]: + short_dataset_name = dataset[1] + if dataset_type == "Phenotypes": + new_type = "Publish" + elif dataset_type == "Genotypes": + new_type = "Geno" + else: + new_type = "ProbeSet" + self.datasets[short_dataset_name] = new_type + + Redis.set("dataset_structure", json.dumps(self.datasets)) # Set LOG_LEVEL_DEBUG=5 to see the following: logger.debugf(5, "datasets",self.datasets) @@ -127,6 +131,7 @@ Publish or ProbeSet. E.g. results = g.db.execute(geno_query).fetchall() if len(results): self.datasets[name] = "ProbeSet" + Redis.set("dataset_structure", json.dumps(self.datasets)) return self.datasets[name] group_name = name.replace("Publish", "") @@ -140,6 +145,7 @@ Publish or ProbeSet. E.g. results = g.db.execute(pheno_query).fetchall() if len(results): self.datasets[name] = "Publish" + Redis.set("dataset_structure", json.dumps(self.datasets)) return self.datasets[name] #ZS: For when there isn't an InfoFiles ID; not sure if this and the preceding query are both necessary @@ -151,6 +157,7 @@ Publish or ProbeSet. E.g. results = g.db.execute(other_pheno_query).fetchall() if len(results): self.datasets[name] = "Publish" + Redis.set("dataset_structure", json.dumps(self.datasets)) return self.datasets[name] geno_query = """ @@ -166,11 +173,11 @@ Publish or ProbeSet. E.g. results = g.db.execute(geno_query).fetchall() if len(results): self.datasets[name] = "Geno" + Redis.set("dataset_structure", json.dumps(self.datasets)) return self.datasets[name] #ZS: It shouldn't ever reach this return None - else: return self.datasets[name] diff --git a/wqflask/wqflask/__init__.py b/wqflask/wqflask/__init__.py index 399e794d..62e98b36 100644 --- a/wqflask/wqflask/__init__.py +++ b/wqflask/wqflask/__init__.py @@ -21,5 +21,5 @@ app.jinja_env.globals.update( numify = formatting.numify ) -import wqflask.views -from wqflask.api import router \ No newline at end of file +from wqflask.api import router +import wqflask.views \ No newline at end of file diff --git a/wqflask/wqflask/api/gen_menu.py b/wqflask/wqflask/api/gen_menu.py index adf66fb5..c7bcb65d 100644 --- a/wqflask/wqflask/api/gen_menu.py +++ b/wqflask/wqflask/api/gen_menu.py @@ -1,7 +1,6 @@ from __future__ import print_function, division import sys -import json from flask import g @@ -23,14 +22,6 @@ def gen_dropdown_json(): types = get_types(groups) datasets = get_datasets(types) - #species.append(('All Species', 'All Species')) - #groups['All Species'] = [('All Groups', 'All Groups')] - #types['All Species'] = {} - #types['All Species']['All Groups'] = [('Phenotypes', 'Phenotypes')] - #datasets['All Species'] = {} - #datasets['All Species']['All Groups'] = {} - #datasets['All Species']['All Groups']['Phenotypes'] = [('All Phenotypes','All Phenotypes')] - data = dict(species=species, groups=groups, types=types, @@ -55,15 +46,6 @@ def get_groups(species): groups = {} for species_name, _species_full_name in species: groups[species_name] = [] - # results = g.db.execute("""SELECT InbredSet.Name, InbredSet.FullName - # FROM InbredSet, Species, ProbeFreeze, GenoFreeze, PublishFreeze - # WHERE Species.Name = '{}' AND - # InbredSet.SpeciesId = Species.Id AND - # (PublishFreeze.InbredSetId = InbredSet.Id OR - # GenoFreeze.InbredSetId = InbredSet.Id OR - # ProbeFreeze.InbredSetId = InbredSet.Id) - # GROUP by InbredSet.Name - # ORDER BY InbredSet.FullName""".format(species_name)).fetchall() results = g.db.execute("""SELECT InbredSet.Name, InbredSet.FullName, IFNULL(InbredSet.Family, 'None') FROM InbredSet, Species diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py index 1d74b699..b22e0004 100644 --- a/wqflask/wqflask/collect.py +++ b/wqflask/wqflask/collect.py @@ -185,7 +185,7 @@ def delete_collection(): if len(uc_id.split(":")) > 1: flash("We've deleted the selected collections.", "alert-info") else: - flash("We've deleted the collection: {}.".format(uc_id), "alert-info") + flash("We've deleted the selected collection.", "alert-info") else: flash("We've deleted the collection: {}.".format(collection_name), "alert-info") diff --git a/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js b/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js index 794804f4..ee7be68c 100644 --- a/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js +++ b/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js @@ -6,6 +6,7 @@ process_json = function(data) { return apply_default(); } }; + $.ajax('/api/v_pre1/gen_dropdown', { dataType: 'json', success: process_json -- cgit v1.2.3 From caa9966df61a9e4290d36af557adc3ede1a3674b Mon Sep 17 00:00:00 2001 From: zsloan Date: Mon, 27 Apr 2020 14:08:30 -0500 Subject: Added timeout for when/if it does the REST API query, so it doesn't hang indefinitely --- wqflask/base/data_set.py | 29 ++++++++++++++++------------- 1 file changed, 16 insertions(+), 13 deletions(-) diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index fd1dff5c..cab708ef 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -98,19 +98,22 @@ Publish or ProbeSet. E.g. if data: self.datasets = json.loads(data) else: #ZS: I don't think this should ever run unless Redis is emptied - data = json.loads(requests.get(GN2_BASE_URL + "/api/v_pre1/gen_dropdown").content) - for species in data['datasets']: - for group in data['datasets'][species]: - for dataset_type in data['datasets'][species][group]: - for dataset in data['datasets'][species][group][dataset_type]: - short_dataset_name = dataset[1] - if dataset_type == "Phenotypes": - new_type = "Publish" - elif dataset_type == "Genotypes": - new_type = "Geno" - else: - new_type = "ProbeSet" - self.datasets[short_dataset_name] = new_type + try: + data = json.loads(requests.get(GN2_BASE_URL + "/api/v_pre1/gen_dropdown", timeout = 5).content) + for species in data['datasets']: + for group in data['datasets'][species]: + for dataset_type in data['datasets'][species][group]: + for dataset in data['datasets'][species][group][dataset_type]: + short_dataset_name = dataset[1] + if dataset_type == "Phenotypes": + new_type = "Publish" + elif dataset_type == "Genotypes": + new_type = "Geno" + else: + new_type = "ProbeSet" + self.datasets[short_dataset_name] = new_type + except: + pass Redis.set("dataset_structure", json.dumps(self.datasets)) -- cgit v1.2.3 From 2fbd5b1283cbbba19edf27ec0109e64ef8bc4723 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Tue, 28 Apr 2020 14:44:02 +0200 Subject: menu --- .../new/javascript/dataset_menu_structure.json | 2617 ++++++++++++++++---- 1 file changed, 2164 insertions(+), 453 deletions(-) diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json index f9bce083..4eb43144 100644 --- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json +++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json @@ -277,6 +277,18 @@ ] }, "CANDLE": { + "Methylation": [ + [ + "423", + "CANDLE_Meth27_0313", + "CANDLE Newborn Cord ILM HumanMethylation27 (Mar13)*" + ], + [ + "422", + "CANDLE_Meth_0313", + "CANDLE Newborn Cord ILM HumanMethylation27 (Mar13) Z-Score*" + ] + ], "Newborn Cord Blood mRNA": [ [ "324", @@ -307,7 +319,7 @@ ] }, "GTEx": { - "Adipose tissue, subcutaneous mRNA": [ + "Adipose Tissue, Subcutaneous mRNA": [ [ "580", "GTEx_log2_Subcu_0314", @@ -319,7 +331,7 @@ "GTEx Human Subcutaneous (Apr14) RPKM" ] ], - "Adipose tissue, visceral mRNA": [ + "Adipose Tissue, Visceral mRNA": [ [ "587", "GTEx_log2_Visce_0314", @@ -873,14 +885,14 @@ ] }, "GTEx_v5": { - "Adipose tissue, subcutaneous mRNA": [ + "Adipose Tissue, Subcutaneous mRNA": [ [ "718", "GTEXv5_AdipSub_0915", "GTEXv5 Human Adipose Subcutaneous RefSeq (Sep15) RPKM log2" ] ], - "Adipose tissue, visceral mRNA": [ + "Adipose Tissue, Visceral mRNA": [ [ "719", "GTEXv5_AdiVis_0915", @@ -1252,359 +1264,875 @@ ] ] }, - "HB": { - "Cerebellum mRNA": [ + "GTEx_v8": { + "Adipose Tissue, Subcutaneous mRNA": [ [ - "326", - "HBTRC-MLC_0611", - "HBTRC-MLC Human Cerebellum Agilent (Jun11) mlratio" + "950", + "GTEXv8_AdipSub_tpm_0220", + "GTEXv8 Human Adipose Subcutaneous RNA-Seq (Feb20) TPM log2" ], [ - "361", - "HBTRC-MLC_N_0611", - "HBTRC-MLC Human Cerebellum Agilent Normal (Jun11) mlratio" + "901", + "GTEXv8_AdipSub_0220", + "GTEXv8 Human Adipose Subcutaneous RNA-Seq (Feb20) log2" + ] + ], + "Adipose Tissue, Visceral mRNA": [ + [ + "951", + "GTEXv8_AdiVis_tpm_0220", + "GTEXv8 Human Adipose Visceral Omentum RNA-Seq (Feb20) TPM log2" ], [ - "362", - "HBTRC-MLC_AD_0611", - "HBTRC-MLC Human Cerebellum Agilent AD (Jun11) mlratio" + "902", + "GTEXv8_AdiVis_0220", + "GTEXv8 Human Adipose Visceral Omentum RNA-Seq (Feb20) log2" + ] + ], + "Adrenal Gland mRNA": [ + [ + "952", + "GTEXv8_AdrGla_tpm_0220", + "GTEXv8 Human Adrenal Gland RNA-Seq (Feb20) TPM log2" ], [ - "363", - "HBTRC-MLC_HD_0611", - "HBTRC-MLC Human Cerebellum Agilent HD (Jun11) mlratio" + "903", + "GTEXv8_AdrGla_0220", + "GTEXv8 Human Adrenal Gland RNA-Seq (Feb20) log2" ] ], - "Prefrontal Cortex mRNA": [ + "Amygdala mRNA": [ [ - "328", - "HBTRC-MLPFC_0611", - "HBTRC-MLC Human Prefrontal Cortex Agilent (Jun11) mlratio" + "956", + "GTEXv8_Amy_tpm_0220", + "GTEXv8 Human Brain Amygdala RNA-Seq (Feb20) TPM log2" ], [ - "367", - "HBTRC-MLPFC_N_0611", - "HBTRC-MLC Human Prefrontal Cortex Agilent Normal (Jun11) mlratio" + "907", + "GTEXv8_Amy_0220", + "GTEXv8 Human Brain Amygdala RNA-Seq (Feb20) log2" + ] + ], + "Anterior Cingulate Cortex mRNA": [ + [ + "957", + "GTEXv8_AntCtx_tpm_0220", + "GTEXv8 Human Brain Anterior cingulate cortex BA24 RNA-Seq (Feb20) TPM log2" ], [ - "368", - "HBTRC-MLPFC_AD_0611", - "HBTRC-MLC Human Prefrontal Cortex Agilent AD (Jun11) mlratio" + "908", + "GTEXv8_AntCtx_0220", + "GTEXv8 Human Brain Anterior cingulate cortex BA24 RNA-Seq (Feb20) log2" + ] + ], + "Aorta mRNA": [ + [ + "953", + "GTEXv8_ArtAor_tpm_0220", + "GTEXv8 Human Artery Aorta RNA-Seq (Feb20) TPM log2" ], [ - "369", - "HBTRC-MLPFC_HD_0611", - "HBTRC-MLC Human Prefrontal Cortex Agilent HD (Jun11) mlratio" + "904", + "GTEXv8_ArtAor_0220", + "GTEXv8 Human Artery Aorta RNA-Seq (Feb20) log2" ] ], - "Primary Visual Cortex mRNA": [ + "Breast - Mammary Tissue mRNA": [ [ - "327", - "HBTRC-MLVC_0611", - "HBTRC-MLC Human Visual Cortex Agilent (Jun11) mlratio" + "969", + "GTEXv8_BrMa_tpm_0220", + "GTEXv8 Human Breast Mammary Tissue RNA-Seq (Feb20) TPM log2" ], [ - "364", - "HBTRC-MLVC_N_0611", - "HBTRC-MLC Human Visual Cortex Agilent Normal (Jun11) mlratio" + "920", + "GTEXv8_BrMa_0220", + "GTEXv8 Human Breast Mammary Tissue RNA-Seq (Feb20) log2" + ] + ], + "Caudate mRNA": [ + [ + "958", + "GTEXv8_BrCa_tpm_0220", + "GTEXv8 Human Brain Caudate basal ganglia RNA-Seq (Feb20) TPM log2" ], [ - "365", - "HBTRC-MLVC_AD_0611", - "HBTRC-MLC Human Visual Cortex Agilent AD (Jun11) mlratio" + "909", + "GTEXv8_BrCa_0220", + "GTEXv8 Human Brain Caudate basal ganglia RNA-Seq (Feb20) log2" + ] + ], + "Cells - EBV-Transformed Lymphocytes mRNA": [ + [ + "970", + "GTEXv8_EBV_tpm_0220", + "GTEXv8 Human Cells-EBV-transformed lymphocytes RNA-Seq (Feb20) TPM log2" ], [ - "366", - "HBTRC-MLVC_HD_0611", - "HBTRC-MLC Human Visual Cortex Agilent HD (Jun11) mlratio" + "921", + "GTEXv8_EBV_0220", + "GTEXv8 Human Cells-EBV-transformed lymphocytes RNA-Seq (Feb20) log2" ] - ] - }, - "HCP": { - "Phenotypes": [ + ], + "Cells - Transformed Fibroblasts mRNA": [ [ - "None", - "HCPPublish", - "HCP Private Phenotypes" + "971", + "GTEXv8_CTF_tpm_0220", + "GTEXv8 Human Cells-Transformed fibroblasts RNA-Seq (Feb20) TPM log2" + ], + [ + "922", + "GTEXv8_CTF_0220", + "GTEXv8 Human Cells-Transformed fibroblasts RNA-Seq (Feb20) log2" ] - ] - }, - "HLC": { - "Liver mRNA": [ + ], + "Cerebellar Cortex mRNA": [ [ - "320", - "HLC_0311", - "GSE9588 Human Liver Normal (Mar11) Both Sexes" + "961", + "GTEXv8_BrCtx_tpm_0220", + "GTEXv8 Human Brain Cortex RNA-Seq (Feb20) TPM log2" ], [ - "384", - "HLCF_0311", - "GSE9588 Human Liver Normal (Mar11) Females" + "912", + "GTEXv8_BrCtx_0220", + "GTEXv8 Human Brain Cortex RNA-Seq (Feb20) log2" + ] + ], + "Cerebellar Hemisphere mRNA": [ + [ + "959", + "GTEXv8_CerH_tpm_0220", + "GTEXv8 Human Brain Cerebellar Hemisphere RNA-Seq (Feb20) TPM log2" ], [ - "383", - "HLCM_0311", - "GSE9588 Human Liver Normal (Mar11) Males" + "910", + "GTEXv8_CerH_0220", + "GTEXv8 Human Brain Cerebellar Hemisphere RNA-Seq (Feb20) log2" ] ], - "Phenotypes": [ + "Cerebellum mRNA": [ [ - "635", - "HLCPublish", - "HLC Published Phenotypes" + "960", + "GTEXv8_BrCe_tpm_0220", + "GTEXv8 Human Brain Cerebellum RNA-Seq (Feb20) TPM log2" + ], + [ + "911", + "GTEXv8_BrCe_0220", + "GTEXv8 Human Brain Cerebellum RNA-Seq (Feb20) log2" ] - ] - }, - "HLT": { - "Lung mRNA": [ + ], + "Colon - Sigmoid mRNA": [ [ - "455", - "GSE23546HLT0613", - "Super Series GSE23546 Whole-Genome GXD Non-Tumorous Human Lung Tissues Affy HuRSTA array (Jun11) RMA" + "972", + "GTEXv8_ColSig_tpm_0220", + "GTEXv8 Human Colon-Sigmoid RNA-Seq (Feb20) TPM log2" ], [ - "454", - "GRNG-GSE23545HLT0613", - "GRNG/GSE23545 Whole-Genome GXD Non-Tumorous Human Lung Tissues Affy HuRSTA array (Jun11) RMA" + "923", + "GTEXv8_ColSig_0220", + "GTEXv8 Human Colon-Sigmoid RNA-Seq (Feb20) log2" ] - ] - }, - "HSB": { - "Amygdala mRNA": [ + ], + "Colon - Transverse mRNA": [ [ - "330", - "KIN_YSM_AMY_0711", - "GN330 Human Amygdala Affy Hu-Exon 1.0 ST (Jul11) Quantile" + "973", + "GTEXv8_ColTra_tpm_0220", + "GTEXv8 Human Colon-Transverse RNA-Seq (Feb20) TPM log2" + ], + [ + "924", + "GTEXv8_ColTra_0220", + "GTEXv8 Human Colon-Transverse RNA-Seq (Feb20) log2" ] ], - "Cerebellar Cortex mRNA": [ + "Coronary mRNA": [ [ - "331", - "KIN_YSM_CBC_0711", - "Human Cerebellar Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + "954", + "GTEXv8_ArtCor_tpm_0220", + "GTEXv8 Human Artery Coronary RNA-Seq (Feb20) TPM log2" + ], + [ + "905", + "GTEXv8_ArtCor_0220", + "GTEXv8 Human Artery Coronary RNA-Seq (Feb20) log2" ] ], - "Dorsolateral Prefrontal Cortex mRNA": [ + "Esophagus - Gastroesophageal mRNA": [ [ - "333", - "KIN_YSM_DFC_0711", - "Human Dorsolateral Prefrontal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + "974", + "GTEXv8_GastJun_tpm_0220", + "GTEXv8 Human Esophagus - Gastroesophageal Junction RNA-Seq (Feb20) TPM log2" + ], + [ + "925", + "GTEXv8_GastJun_0220", + "GTEXv8 Human Esophagus - Gastroesophageal Junction RNA-Seq (Feb20) log2" ] ], - "Hippocampus mRNA": [ + "Esophagus - Mucosa mRNA": [ [ - "337", - "KIN_YSM_HIP_0711", - "Human Hippocampus Affy Hu-Exon 1.0 ST (Jul11) Quantile" + "975", + "GTEXv8_EsoMu_tpm_0220", + "GTEXv8 Human Esophagus-Mucosa RNA-Seq (Feb20) TPM log2" + ], + [ + "926", + "GTEXv8_EsoMu_0220", + "GTEXv8 Human Esophagus-Mucosa RNA-Seq (Feb20) log2" ] ], - "Inferior Temporal Cortex mRNA": [ + "Esophagus - Muscularis mRNA": [ [ - "339", - "KIN_YSM_ITC_0711", - "Human Inferior Temporal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + "976", + "GTEXv8_EsoMus_tpm_0220", + "GTEXv8 Human Esophagus-Muscularis RNA-Seq (Feb20) TPM log2" + ], + [ + "927", + "GTEXv8_EsoMus_0220", + "GTEXv8 Human Esophagus-Muscularis RNA-Seq (Feb20) log2" ] ], - "Medial Prefrontal Cortex mRNA": [ + "Frontal Cortex mRNA": [ [ - "343", - "KIN_YSM_MFC_0711", - "Human Medial Prefrontal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + "962", + "GTEXv8_BrFr_tpm_0220", + "GTEXv8 Human Brain Frontal Cortex BA9 RNA-Seq (Feb20) TPM log2" + ], + [ + "913", + "GTEXv8_BrFr_0220", + "GTEXv8 Human Brain Frontal Cortex BA9 RNA-Seq (Feb20) log2" ] ], - "Mediodorsal Nucleus of Thalamus mRNA": [ + "Heart - Atrial Appendage mRNA": [ [ - "342", - "KIN_YSM_MD_0711", - "Human Mediodorsal Nucleus of Thalamus Affy Hu-Exon 1.0 ST (Jul11) Quantile" + "977", + "GTEXv8_HAA_tpm_0220", + "GTEXv8 Human Heart-Atrial Appendage RNA-Seq (Feb20) TPM log2" + ], + [ + "928", + "GTEXv8_HAA_0220", + "GTEXv8 Human Heart-Atrial Appendage RNA-Seq (Feb20) log2" ] ], - "Orbital Prefrontal Cortex mRNA": [ + "Heart - Left Ventricle mRNA": [ [ - "347", - "KIN_YSM_OFC_0711", - "Human Orbital Prefrontal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + "978", + "GTEXv8_LV_tpm_0220", + "GTEXv8 Human Heart-Left Ventricle RNA-Seq (Feb20) TPM log2" + ], + [ + "929", + "GTEXv8_LV_0220", + "GTEXv8 Human Heart-Left Ventricle RNA-Seq (Feb20) log2" ] ], - "Phenotypes": [ + "Hippocampus mRNA": [ [ - "None", - "HSBPublish", - "HSB Published Phenotypes" + "963", + "GTEXv8_Hip_tpm_0220", + "GTEXv8 Human Brain Hippocampus RNA-Seq (Feb20) TPM log2" + ], + [ + "914", + "GTEXv8_Hip_0220", + "GTEXv8 Human Brain Hippocampus RNA-Seq (Feb20) log2" ] ], - "Posterior Inferior Parietal Cortex mRNA": [ + "Hypothalamus mRNA": [ [ - "338", - "KIN_YSM_IPC_0711", - "Human Posterior Inferior Parietal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + "964", + "GTEXv8_Hiptha_tpm_0220", + "GTEXv8 Human Brain Hypothalamus RNA-Seq (Feb20) TPM log2" + ], + [ + "915", + "GTEXv8_Hiptha_0220", + "GTEXv8 Human Brain Hypothalamus RNA-Seq (Feb20) log2" ] ], - "Posterior Superior Temporal Cortex mRNA": [ + "Kidney mRNA": [ [ - "350", - "KIN_YSM_STC_0711", - "Human Posterior Superior Temporal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + "979", + "GTEXv8_Kidn_tpm_0220", + "GTEXv8 Human Kidney-Cortex RNA-Seq (Feb20) TPM log2" + ], + [ + "930", + "GTEXv8_Kidn_0220", + "GTEXv8 Human Kidney-Cortex RNA-Seq (Feb20) log2" ] ], - "Primary Auditory (A1) Cortex mRNA": [ + "Liver mRNA": [ [ - "329", - "KIN_YSM_A1C_0711", - "Human Primary Auditory (A1) Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + "980", + "GTEXv8_Liv_tpm_0220", + "GTEXv8 Human Liver RNA-Seq (Feb20) TPM log2" + ], + [ + "931", + "GTEXv8_Liv_0220", + "GTEXv8 Human Liver RNA-Seq (Feb20) log2" ] ], - "Primary Motor (M1) Cortex mRNA": [ + "Lung mRNA": [ [ - "341", - "KIN_YSM_M1C_0711", - "Human Primary Motor (M1) Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + "981", + "GTEXv8_Lung_tpm_0220", + "GTEXv8 Human Lung RNA-Seq (Feb20) TPM log2" + ], + [ + "932", + "GTEXv8_Lung_0220", + "GTEXv8 Human Lung RNA-Seq (Feb20) log2" ] ], - "Primary Somatosensory (S1) Cortex mRNA": [ + "Muscle mRNA": [ [ - "349", - "KIN_YSM_S1C_0711", - "Human Primary Somatosensory (S1) Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + "982", + "GTEXv8_MuSk_tpm_0220", + "GTEXv8 Human Muscle-Skeletal RNA-Seq (Feb20) TPM log2" + ], + [ + "933", + "GTEXv8_MuSk_0220", + "GTEXv8 Human Muscle-Skeletal RNA-Seq (Feb20) log2" ] ], - "Primary Visual Cortex mRNA": [ + "Nerve - Tibial mRNA": [ [ - "354", - "KIN_YSM_V1C_0711", - "Human Primary Visual Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + "983", + "GTEXv8_Tib_tpm_0220", + "GTEXv8 Human Nerve-Tibial RNA-Seq (Feb20) TPM log2" + ], + [ + "934", + "GTEXv8_Tib_0220", + "GTEXv8 Human Nerve-Tibial RNA-Seq (Feb20) log2" ] ], - "Striatum mRNA": [ + "Nucleus Accumbens mRNA": [ [ - "351", - "KIN_YSM_STR_0711", - "Human Striatum Affy Hu-Exon 1.0 ST (Jul11) Quantile" + "965", + "GTEXv8_NuAcc_tpm_0220", + "GTEXv8 Human Brain Nucleus accumbens basal ganglia RNA-Seq (Feb20) TPM log2" + ], + [ + "916", + "GTEXv8_NuAcc_0220", + "GTEXv8 Human Brain Nucleus accumbens basal ganglia RNA-Seq (Feb20) log2" ] ], - "Ventrolateral Prefrontal Cortex mRNA": [ + "Ovary mRNA": [ [ - "356", - "KIN_YSM_VFC_0711", - "Human Ventrolateral Prefrontal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + "984", + "GTEXv8_Ov_tpm_0220", + "GTEXv8 Human Ovary RNA-Seq (Feb20) TPM log2" + ], + [ + "935", + "GTEXv8_Ov_0220", + "GTEXv8 Human Ovary RNA-Seq (Feb20) log2" ] - ] - }, - "Islets-Gerling": { + ], + "Pancreas mRNA": [ + [ + "985", + "GTEXv8_Panc_tpm_0220", + "GTEXv8 Human Pancreas RNA-Seq (Feb20) TPM log2" + ], + [ + "936", + "GTEXv8_Panc_0220", + "GTEXv8 Human Pancreas RNA-Seq (Feb20) log2" + ] + ], "Phenotypes": [ [ "None", - "Islets-GerlingPublish", - "Islets-Gerling Phenotypes" + "GTEx_v8Publish", + "GTEx_v8 Phenotypes" ] - ] - }, - "TIGEM-Retina-RNA-Seq": { + ], + "Pituitary Gland mRNA": [ + [ + "986", + "GTEXv8_Pit_tpm_0220", + "GTEXv8 Human Pituitary RNA-Seq (Feb20) TPM log2" + ], + [ + "937", + "GTEXv8_Pit_0220", + "GTEXv8 Human Pituitary RNA-Seq (Feb20) log2" + ] + ], + "Prostate mRNA": [ + [ + "987", + "GTEXv8_Prost_tpm_0220", + "GTEXv8 Human Prostate RNA-Seq (Feb20) TPM log2" + ], + [ + "938", + "GTEXv8_Prost_0220", + "GTEXv8 Human Prostate RNA-Seq (Feb20) log2" + ] + ], + "Putamen mRNA": [ + [ + "966", + "GTEXv8_PutB_tpm_0220", + "GTEXv8 Human Brain Putamen basal ganglia RNA-Seq (Feb20) TPM log2" + ], + [ + "917", + "GTEXv8_PutB_0220", + "GTEXv8 Human Brain Putamen basal ganglia RNA-Seq (Feb20) log2" + ] + ], + "Salivary Gland mRNA": [ + [ + "988", + "GTEXv8_SalGl_tpm_0220", + "GTEXv8 Human Salivary Gland Minor RNA-Seq (Feb20) TPM log2" + ], + [ + "939", + "GTEXv8_SalGl_0220", + "GTEXv8 Human Salivary Gland Minor RNA-Seq (Feb20) log2" + ] + ], + "Skin - Not Sun Exposed (Suprapubic) mRNA": [ + [ + "989", + "GTEXv8_SkN_tpm_0220", + "GTEXv8 Human Skin-Not Sun Exposed-Suprapubic RNA-Seq (Feb20) TPM log2" + ], + [ + "940", + "GTEXv8_SkN_0220", + "GTEXv8 Human Skin-Not Sun Exposed-Suprapubic RNA-Seq (Feb20) log2" + ] + ], + "Skin - Sun Exposed (Lower leg) mRNA": [ + [ + "990", + "GTEXv8_SkS_tpm_0220", + "GTEXv8 Human Skin-Sun Exposed-Lower leg RNA-Seq (Feb20) TPM log2" + ], + [ + "941", + "GTEXv8_SkS_0220", + "GTEXv8 Human Skin-Sun Exposed-Lower leg RNA-Seq (Feb20) log2" + ] + ], + "Small Intestine - Terminal Ileum mRNA": [ + [ + "997", + "GTEXv8_SInt_tpm_0220", + "GTEXv8 Human Small Intestine - Terminal Ileum RNA-Seq (Feb20) TPM log2" + ], + [ + "948", + "GTEXv8_SInt_0220", + "GTEXv8 Human Small Intestine - Terminal Ileum RNA-Seq (Feb20) log2" + ] + ], + "Spinal Cord mRNA": [ + [ + "967", + "GTEXv8_SpCo_tpm_0220", + "GTEXv8 Human Brain Spinal cord cervical c-1 RNA-Seq (Feb20) TPM log2" + ], + [ + "918", + "GTEXv8_SpCo_0220", + "GTEXv8 Human Brain Spinal cord cervical c-1 RNA-Seq (Feb20) log2" + ] + ], + "Spleen mRNA": [ + [ + "991", + "GTEXv8_Sple_tpm_0220", + "GTEXv8 Human Spleen RNA-Seq (Feb20) TPM log2" + ], + [ + "942", + "GTEXv8_Sple_0220", + "GTEXv8 Human Spleen RNA-Seq (Feb20) log2" + ] + ], + "Stomach mRNA": [ + [ + "992", + "GTEXv8_Sto_tpm_0220", + "GTEXv8 Human Stomach RNA-Seq (Feb20) TPM log2" + ], + [ + "943", + "GTEXv8_Sto_0220", + "GTEXv8 Human Stomach RNA-Seq (Feb20) log2" + ] + ], + "Substantia Nigra mRNA": [ + [ + "968", + "GTEXv8_SubN_tpm_0220", + "GTEXv8 Human Brain Substantia nigra RNA-Seq (Feb20) TPM log2" + ], + [ + "919", + "GTEXv8_SubN_0220", + "GTEXv8 Human Brain Substantia nigra RNA-Seq (Feb20) log2" + ] + ], + "Testis mRNA": [ + [ + "993", + "GTEXv8_Test_tpm_0220", + "GTEXv8 Human Testis RNA-Seq (Feb20) TPM log2" + ], + [ + "944", + "GTEXv8_Test_0220", + "GTEXv8 Human Testis RNA-Seq (Feb20) log2" + ] + ], + "Thyroid mRNA": [ + [ + "994", + "GTEXv8_Thy_tpm_0220", + "GTEXv8 Human Thyroid RNA-Seq (Feb20) TPM log2" + ], + [ + "945", + "GTEXv8_Thy_0220", + "GTEXv8 Human Thyroid RNA-Seq (Feb20) log2" + ] + ], + "Tibial mRNA": [ + [ + "955", + "GTEXv8_ArtTib_tpm_0220", + "GTEXv8 Human Artery Tibial RNA-Seq (Feb20) TPM log2" + ], + [ + "906", + "GTEXv8_ArtTib_0220", + "GTEXv8 Human Artery Tibial RNA-Seq (Feb20) log2" + ] + ], + "Uterus mRNA": [ + [ + "995", + "GTEXv8_Ut_tpm_0220", + "GTEXv8 Human Uterus RNA-Seq (Feb20) TPM log2" + ], + [ + "946", + "GTEXv8_Ut_0220", + "GTEXv8 Human Uterus RNA-Seq (Feb20) log2" + ] + ], + "Vagina mRNA": [ + [ + "996", + "GTEXv8_Vag_tpm_0220", + "GTEXv8 Human Vagina RNA-Seq (Feb20) TPM log2" + ], + [ + "947", + "GTEXv8_Vag_0220", + "GTEXv8 Human Vagina RNA-Seq (Feb20) log2" + ] + ], + "Whole Blood mRNA": [ + [ + "998", + "GTEXv8_Wbl_tpm_0220", + "GTEXv8 Human Whole Blood RNA-Seq (Feb20) TPM log2" + ], + [ + "949", + "GTEXv8_Wbl_0220", + "GTEXv8 Human Whole Blood RNA-Seq (Feb20) log2" + ] + ] + }, + "HB": { + "Cerebellum mRNA": [ + [ + "326", + "HBTRC-MLC_0611", + "HBTRC-MLC Human Cerebellum Agilent (Jun11) mlratio" + ], + [ + "361", + "HBTRC-MLC_N_0611", + "HBTRC-MLC Human Cerebellum Agilent Normal (Jun11) mlratio" + ], + [ + "362", + "HBTRC-MLC_AD_0611", + "HBTRC-MLC Human Cerebellum Agilent AD (Jun11) mlratio" + ], + [ + "363", + "HBTRC-MLC_HD_0611", + "HBTRC-MLC Human Cerebellum Agilent HD (Jun11) mlratio" + ] + ], + "Prefrontal Cortex mRNA": [ + [ + "328", + "HBTRC-MLPFC_0611", + "HBTRC-MLC Human Prefrontal Cortex Agilent (Jun11) mlratio" + ], + [ + "367", + "HBTRC-MLPFC_N_0611", + "HBTRC-MLC Human Prefrontal Cortex Agilent Normal (Jun11) mlratio" + ], + [ + "368", + "HBTRC-MLPFC_AD_0611", + "HBTRC-MLC Human Prefrontal Cortex Agilent AD (Jun11) mlratio" + ], + [ + "369", + "HBTRC-MLPFC_HD_0611", + "HBTRC-MLC Human Prefrontal Cortex Agilent HD (Jun11) mlratio" + ] + ], + "Primary Visual Cortex mRNA": [ + [ + "327", + "HBTRC-MLVC_0611", + "HBTRC-MLC Human Visual Cortex Agilent (Jun11) mlratio" + ], + [ + "364", + "HBTRC-MLVC_N_0611", + "HBTRC-MLC Human Visual Cortex Agilent Normal (Jun11) mlratio" + ], + [ + "365", + "HBTRC-MLVC_AD_0611", + "HBTRC-MLC Human Visual Cortex Agilent AD (Jun11) mlratio" + ], + [ + "366", + "HBTRC-MLVC_HD_0611", + "HBTRC-MLC Human Visual Cortex Agilent HD (Jun11) mlratio" + ] + ] + }, + "HCP": { "Phenotypes": [ [ "None", - "TIGEM-Retina-RNA-SeqPublish", - "TIGEM-Retina-RNA-Seq Phenotypes" + "HCPPublish", + "HCP Private Phenotypes" + ] + ] + }, + "HLC": { + "Liver mRNA": [ + [ + "320", + "HLC_0311", + "GSE9588 Human Liver Normal (Mar11) Both Sexes" + ], + [ + "384", + "HLCF_0311", + "GSE9588 Human Liver Normal (Mar11) Females" + ], + [ + "383", + "HLCM_0311", + "GSE9588 Human Liver Normal (Mar11) Males" ] ], - "Retina mRNA": [ + "Phenotypes": [ [ - "802", - "TIGEM_hg38_ret_rna-seq_0916", - "TIGEM Human Retina RNA-Seq (Sep16) RPKM log2" + "635", + "HLCPublish", + "HLC Published Phenotypes" ] ] - } - }, - "mouse": { - "AIL": { - "Genotypes": [ + }, + "HLT": { + "Lung mRNA": [ [ - "None", - "AILGeno", - "AIL Genotypes" + "455", + "GSE23546HLT0613", + "Super Series GSE23546 Whole-Genome GXD Non-Tumorous Human Lung Tissues Affy HuRSTA array (Jun11) RMA" + ], + [ + "454", + "GRNG-GSE23545HLT0613", + "GRNG/GSE23545 Whole-Genome GXD Non-Tumorous Human Lung Tissues Affy HuRSTA array (Jun11) RMA" + ] + ] + }, + "HSB": { + "Amygdala mRNA": [ + [ + "330", + "KIN_YSM_AMY_0711", + "GN330 Human Amygdala Affy Hu-Exon 1.0 ST (Jul11) Quantile" + ] + ], + "Cerebellar Cortex mRNA": [ + [ + "331", + "KIN_YSM_CBC_0711", + "Human Cerebellar Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + ] + ], + "Dorsolateral Prefrontal Cortex mRNA": [ + [ + "333", + "KIN_YSM_DFC_0711", + "Human Dorsolateral Prefrontal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" ] ], "Hippocampus mRNA": [ [ - "874", - "UCSD_AIL_HIP_RNA-Seq_log2_0418", - "UCSD AIL Hippocampus (Apr18) RNA-Seq Log2" - ], + "337", + "KIN_YSM_HIP_0711", + "Human Hippocampus Affy Hu-Exon 1.0 ST (Jul11) Quantile" + ] + ], + "Inferior Temporal Cortex mRNA": [ [ - "844", - "UCSD_AIL_HIP_RNA-Seq_0418", - "UCSD AIL Hippocampus (Apr18) RNA-Seq" + "339", + "KIN_YSM_ITC_0711", + "Human Inferior Temporal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + ] + ], + "Medial Prefrontal Cortex mRNA": [ + [ + "343", + "KIN_YSM_MFC_0711", + "Human Medial Prefrontal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + ] + ], + "Mediodorsal Nucleus of Thalamus mRNA": [ + [ + "342", + "KIN_YSM_MD_0711", + "Human Mediodorsal Nucleus of Thalamus Affy Hu-Exon 1.0 ST (Jul11) Quantile" + ] + ], + "Orbital Prefrontal Cortex mRNA": [ + [ + "347", + "KIN_YSM_OFC_0711", + "Human Orbital Prefrontal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + ] + ], + "Phenotypes": [ + [ + "None", + "HSBPublish", + "HSB Published Phenotypes" + ] + ], + "Posterior Inferior Parietal Cortex mRNA": [ + [ + "338", + "KIN_YSM_IPC_0711", + "Human Posterior Inferior Parietal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + ] + ], + "Posterior Superior Temporal Cortex mRNA": [ + [ + "350", + "KIN_YSM_STC_0711", + "Human Posterior Superior Temporal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + ] + ], + "Primary Auditory (A1) Cortex mRNA": [ + [ + "329", + "KIN_YSM_A1C_0711", + "Human Primary Auditory (A1) Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" ] ], - "Phenotypes": [ + "Primary Motor (M1) Cortex mRNA": [ [ - "653", - "AILPublish", - "AIL Phenotypes" + "341", + "KIN_YSM_M1C_0711", + "Human Primary Motor (M1) Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" ] ], - "Prefrontal Cortex mRNA": [ + "Primary Somatosensory (S1) Cortex mRNA": [ [ - "876", - "UCSD_AIL_PFC_RNA-Seq_log2_0418", - "UCSD AIL Prefrontal Cortex (Apr18) RNA-Seq Log2" - ], + "349", + "KIN_YSM_S1C_0711", + "Human Primary Somatosensory (S1) Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + ] + ], + "Primary Visual Cortex mRNA": [ [ - "846", - "UCSD_AIL_PFC_RNA-Seq_0418", - "UCSD AIL Prefrontal Cortex (Apr18) RNA-Seq" + "354", + "KIN_YSM_V1C_0711", + "Human Primary Visual Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" ] ], "Striatum mRNA": [ [ - "875", - "UCSD_AIL_STR_RNA-Seq_log2_0418", - "UCSD AIL Striatum (Apr18) RNA-Seq Log2" - ], + "351", + "KIN_YSM_STR_0711", + "Human Striatum Affy Hu-Exon 1.0 ST (Jul11) Quantile" + ] + ], + "Ventrolateral Prefrontal Cortex mRNA": [ [ - "845", - "UCSD_AIL_STR_RNA-Seq_0418", - "UCSD AIL Striatum (Apr18) RNA-Seq" + "356", + "KIN_YSM_VFC_0711", + "Human Ventrolateral Prefrontal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" ] ] }, - "AIL-LGSM-F34-A": { - "Phenotypes": [ + "Islets-Gerling": { + "Islets mRNA": [ [ - "655", - "AIL-LGSM-F34-APublish", - "AIL F34-A Phenotypes" + "824", + "UTHSC_HuIslets_Mar17", + "UTHSC Human Islets Affy Human Gene 2.0 ST (Mar17) RMA" ] - ] - }, - "AIL-LGSM-F34-F39-43-GBS": { + ], "Phenotypes": [ [ - "654", - "AIL-LGSM-F34-F39-43-GBSPublish", - "AIL F34-F39-43-GBS Phenotypes" + "None", + "Islets-GerlingPublish", + "Islets-Gerling Phenotypes" ] ] }, - "AIL-LGSM-F34-GBS": { + "TIGEM-Retina-RNA-Seq": { "Phenotypes": [ [ - "656", - "AIL-LGSM-F34-GBSPublish", - "AIL F34-GBS Phenotypes" + "None", + "TIGEM-Retina-RNA-SeqPublish", + "TIGEM-Retina-RNA-Seq Phenotypes" ] - ] - }, - "AIL-LGSM-F39-43-GBS": { - "Phenotypes": [ + ], + "Retina mRNA": [ [ - "657", - "AIL-LGSM-F39-43-GBSPublish", - "AIL F39-43-GBS Phenotypes" + "802", + "TIGEM_hg38_ret_rna-seq_0916", + "TIGEM Human Retina RNA-Seq (Sep16) RPKM log2" ] ] - }, + } + }, + "mouse": { "AKXD": { "Genotypes": [ [ @@ -1685,6 +2213,22 @@ ] ] }, + "B6-Lens": { + "Ocular Lens mRNA": [ + [ + "999", + "MouseB6Lens_rma_0220", + "Mouse Ocular Lens Developmental Timecourse (Feb20) RMA" + ] + ], + "Phenotypes": [ + [ + "None", + "B6-LensPublish", + "B6-Lens Phenotypes" + ] + ] + }, "B6BTBRF2": { "Genotypes": [ [ @@ -1720,6 +2264,25 @@ "B6D2Publish", "UTHSC-Glaucoma-Aged-Retina Phenotypes" ] + ], + "Retina mRNA": [ + [ + "803", + "UTHSC_mm9_B6D2_Ret_0916", + "UTHSC B6D2 Retina Affy MoGene 1.0ST (Sep16) Gene Level RMA" + ], + [ + "804", + "UTHSC_mm9_B6D2_RetEx_0916", + "UTHSC B6D2 Retina Affy MoGene 1.0ST (Sep16) Exon Level RMA" + ] + ], + "Retina microRNA": [ + [ + "806", + "UTHSC_mm10_B6D2_Ret_miRNA_1116", + "UTHSC B6D2 Retina Affy miRNA-4.0 (Nov16) RMA" + ] ] }, "B6D2F2": { @@ -1771,6 +2334,28 @@ "B6D2F2-PSU Genotypes" ] ], + "Muscle mRNA": [ + [ + "134", + "PSU-B6D2F2_0812", + "PSU B6D2F2 Muscle Affy Mouse Genome 430 2.0 (Aug12) RMA" + ], + [ + "404", + "PSU-B6D2F2_F0812", + "PSU B6D2F2 Muscle Affy Mouse Genome 430 2.0 (Aug12) RMA Females" + ], + [ + "405", + "PSU-B6D2F2_M0812", + "PSU B6D2F2 Muscle Affy Mouse Genome 430 2.0 (Aug12) RMA Males" + ], + [ + "406", + "PSU-B6D2F2_M2000812", + "PSU B6D2F2 Muscle Affy Mouse Genome 430 2.0 (Aug12) RMA Males Aged 200*" + ] + ], "Phenotypes": [ [ "None", @@ -1906,6 +2491,23 @@ "UCLA BHF2 Liver (June05) mlratio" ] ], + "Muscle mRNA": [ + [ + "203", + "UCLA_BHF2_MUSCLE_FEMALE", + "UCLA BHF2 Muscle Female mlratio*" + ], + [ + "202", + "UCLA_BHF2_MUSCLE_MALE", + "UCLA BHF2 Muscle Male mlratio*" + ], + [ + "168", + "UCLA_BHF2_MUSCLE_0605", + "UCLA BHF2 Muscle (June05) mlratio*" + ] + ], "Phenotypes": [ [ "None", @@ -2090,6 +2692,26 @@ "414", "UCLA_BXD-on_Femur_0113_RSN", "UCLA GSE27483 BXD Only Bone Femur ILM Mouse WG-6 v1.1 (Jan13) RSN" + ], + [ + "464", + "UTHSCWGU88BFMG1013", + "UTHSC WGU88 Male Bone Femur AFFY Mouse Gene ST 2.0 Gene Level (Oct13) RMA" + ], + [ + "465", + "UTHSCWGU88BFMEx1013", + "UTHSC WGU88 Male Bone Femur AFFY Mouse Gene ST 2.0 Exon Level (Oct13) RMA" + ], + [ + "466", + "UTHSCWGU88BFFG1013", + "UTHSC WGU88 Female Bone Femur AFFY Mouse Gene ST 2.0 Gene Level (Oct13) RMA" + ], + [ + "467", + "UTHSCWGU88BFFEx1013", + "UTHSC WGU88 Female Bone Femur AFFY Mouse Gene ST 2.0 Exon Level (Oct13) RMA" ] ], "Brain mRNA": [ @@ -2221,6 +2843,76 @@ "9", "CB_M_1003_M", "SJUT Cerebellum mRNA M430 (Oct03) MAS5" + ], + [ + "436", + "CMMTUBCBXDCerILM0513", + "UBC/CMMT BXD Cerebellum All Ages Combined ILM Mouse WG-6 v2.0 (May13) RankInv" + ], + [ + "441", + "CMMTUBCBXDG12CerILM0513", + "UBC/CMMT BXD E12 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv" + ], + [ + "442", + "CMMTUBCBXDG15CerILM0513", + "UBC/CMMT BXD E15 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv" + ], + [ + "443", + "CMMTUBCBXDG18CerILM0513", + "UBC/CMMT BXD E18 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv" + ], + [ + "437", + "CMMTUBCBXDP00CerILM0513", + "UBC/CMMT BXD P0 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv" + ], + [ + "438", + "CMMTUBCBXDP03CerILM0513", + "UBC/CMMT BXD P3 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv" + ], + [ + "439", + "CMMTUBCBXDP06CerILM0513", + "UBC/CMMT BXD P6 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv" + ], + [ + "440", + "CMMTUBCBXDP09CerILM0513", + "UBC/CMMT BXD P9 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv" + ], + [ + "415", + "GenEx_BXD_CerebEt_RMA_0213", + "GenEx BXD EtOH Cerebellum Affy M430 2.0 (Feb13) RMA Both Sexes" + ], + [ + "416", + "GenEx_BXD_CerebEt_RMA_F_0213", + "GenEx BXD EtOH Cerebellum Affy M430 2.0 (Feb13) RMA Females" + ], + [ + "417", + "GenEx_BXD_CerebEt_RMA_M_0213", + "GenEx BXD EtOH Cerebellum Affy M430 2.0 (Feb13) RMA Males" + ], + [ + "418", + "GenEx_BXD_CerebSal_RMA_0213", + "GenEx BXD Sal Cerebellum Affy M430 2.0 (Feb13) RMA Both Sexes" + ], + [ + "419", + "GenEx_BXD_CerebSal_RMA_F_0213", + "GenEx BXD Sal Cerebellum Affy M430 2.0 (Feb13) RMA Females" + ], + [ + "420", + "GenEx_BXD_CerebSal_RMA_M_0213", + "GenEx BXD Sal Cerebellum Affy M430 2.0 (Feb13) RMA Males" ] ], "Eye mRNA": [ @@ -2297,6 +2989,21 @@ "597", "UTHSC_GutExL_0414", "UTHSC Mouse BXD Gastrointestinal Affy MoGene 1.0 ST Exon Level (Apr14) RMA" + ], + [ + "839", + "EPFL-LISP_BXD_Col-CD+HFD0917", + "EPFL/LISP BXD CD+HFD Gastrointestinal Affy Clariom S GeneLevel Main (Sep17) RMA" + ], + [ + "841", + "EPFL-LISP_BXD_Col-HFD0917", + "EPFL/LISP BXD HFD Gastrointestinal Affy Clariom S GeneLevel Main (Sep17) RMA" + ], + [ + "840", + "EPFL-LISP_BXD_Col-CD0917", + "EPFL/LISP BXD CD Gastrointestinal Affy Clariom S GeneLevel Main (Sep17) RMA" ] ], "Genotypes": [ @@ -2502,6 +3209,23 @@ "711", "UTHSC_BXD_AgeHipp0515", "UTHSC BXD Aged Hippocampus Affy MoGene1.0 ST (May15) RMA Gene Level" + ], + [ + "393", + "UTHSC_BXD_HArev3_0912", + "UTHSC BXD Aged Hippocampus rev3 Affy Mouse Gene 1.0 ST (Sep12) RMA" + ], + [ + "392", + "UTHSC_BXD_H_0912", + "UTHSC BXD Aged Hippocampus Affy Mouse Gene 1.0 ST (Sep12) RMA Exon Level" + ] + ], + "Hippocampus microRNA": [ + [ + "491", + "UTHSC_BXD_Hip_miRNASeq0214", + "UTHSC BXD Hippocampus Ion Torrent microRNA (Feb14) RPKM*" ] ], "Hypothalamus mRNA": [ @@ -2578,6 +3302,30 @@ "Mouse Kidney M430v2 (Jul06) PDNN" ] ], + "Leucocytes mRNA": [ + [ + "218", + "Illum_BXD_PBL_1108", + "UWA Illumina PBL (Nov08) RSN*" + ] + ], + "Liver DNAm": [ + [ + "891", + "UTHSC-BXD-LivDNAm-1119", + "UTHSC BXD Liver CD-HFD DNAm (Nov19) Sesame" + ], + [ + "892", + "UTHSC-BXD-LivHFDNAm-1119", + "UTHSC BXD Liver HFD DNAm (Nov19) Sesame" + ], + [ + "893", + "UTHSC-BXD-LivCDNAm-1119", + "UTHSC BXD Liver CD DNAm (Nov19) Sesame" + ] + ], "Liver Metabolome": [ [ "835", @@ -2616,6 +3364,21 @@ ] ], "Liver Proteome": [ + [ + "887", + "EPFL-ETHZ-BXD-LivProtAvg-CD-HF-1119", + "EPFL/ETHZ BXD Liver Proteome CD+HFD (Nov19)" + ], + [ + "888", + "EPFL-ETHZ-BXD-LivProtAvg-CD-1119", + "EPFL/ETHZ BXD Liver Proteome CD (Nov19)" + ], + [ + "889", + "EPFL-ETHZ-BXD-LivProtAvg-HFD-1119", + "EPFL/ETHZ BXD Liver Proteome HFD (Nov19)" + ], [ "540", "EPFLETHZBXDprotCD0514", @@ -2683,6 +3446,21 @@ "NIA-AgBXD-Liv_CD-rna-seq-0818", "NIA Aging BXD CD Liver RNA-Seq (Aug18) Log2" ], + [ + "851", + "NIA-AgBXD-Liv_CDHFD-0818", + "NIA Aging BXD CD+HFD Liver Affy Clariom S Gene Level (Aug18) RMA" + ], + [ + "852", + "NIA-AgBXD-Liv_HFD-0818", + "NIA Aging BXD HFD Liver Affy Clariom S Gene Level (Aug18) RMA" + ], + [ + "853", + "NIA-AgBXD-Liv_CD-0818", + "NIA Aging BXD CD Liver Affy Clariom S Gene Level (Aug18) RMA" + ], [ "818", "UCLA_BXD_Liv_Jan16", @@ -2698,6 +3476,11 @@ "EPFLMouseLiverHFDRMA0413", "EPFL/LISP BXD HFD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA" ], + [ + "849", + "EPFLMouseLiverCDEx0413", + "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level" + ], [ "848", "EPFLMouseLiverHFCEx0413", @@ -2708,11 +3491,6 @@ "EPFLMouseLiverCDRMA0413", "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA" ], - [ - "849", - "EPFLMouseLiverCDEx0413", - "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level" - ], [ "433", "EPFLMouseLiverBothExRMA0413", @@ -2799,6 +3577,26 @@ "161", "HZI_0408_M", "HZI Lung M430v2 (Apr08) MAS5" + ], + [ + "807", + "HZI_LungBXD_RNA-Seq_1116", + "HZI Lung Flu Infected BXD (Nov16) RNA-Seq*" + ], + [ + "598", + "HZI_PR8M-F_1014", + "HZI PR8M-Infected Lungs Females RNAseq (Oct14) RPKM Log2*" + ], + [ + "387", + "HZI_PR8M_Q_0612", + "HZI PR8M-Infected Lungs Agilent4x44 (Apr12) Quantile Females" + ], + [ + "424", + "HZI_LTCF_0313", + "HZI Lung Time Course Flu PR8M (Mar13) Schughart*" ] ], "Midbrain mRNA": [ @@ -2808,6 +3606,23 @@ "VU BXD Midbrain Agilent SurePrint G3 Mouse GE (May12) Quantile" ] ], + "Muscle Metabolome": [ + [ + "476", + "EPFL-LISP_MusPMetCDHFD1213", + "EPFL/LISP BXD Muscle Polar Metabolites CD+HFD (Jun14)" + ], + [ + "477", + "EPFL-LISP_MusPMetHFD1213", + "EPFL/LISP BXD Muscle Polar Metabolites HFD (Jun14)" + ], + [ + "478", + "EPFL-LISP_MusPMetCD1213", + "EPFL/LISP BXD Muscle Polar Metabolites CD (Jun14)" + ] + ], "Muscle mRNA": [ [ "378", @@ -2877,11 +3692,68 @@ "BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov10) RankInv" ] ], + "Neutrophils mRNA": [ + [ + "595", + "UTHSC-Neut-1014", + "UTHSC Elicited Peritoneal Neutrophils Affy MoGene 2.0 ST (Oct14) RMA" + ], + [ + "596", + "UTHSC-Neut_EL-1014", + "UTHSC Elicited Peritoneal Neutrophils Affy MoGene 2.0 ST (Oct14) RMA Exon Level" + ] + ], "Nucleus Accumbens mRNA": [ [ "156", "VCUSalo_1007_R", "VCU BXD NAc Sal M430 2.0 (Oct07) RMA" + ], + [ + "792", + "VCU_BXD_Nac_CIE_Air_0416", + "VCU BXD NAc CIE Air Masked ComBat M430 2.0 (Apr16) RMA" + ], + [ + "793", + "VCU_BXD_Nac_CIE_AirZ_0416", + "VCU BXD NAc CIE Air Masked ComBat M430 2.0 (Apr16) RMA Z-score" + ], + [ + "794", + "VCU_BXD_Nac_CIE_Et_0416", + "VCU BXD NAc CIE EtOH Masked ComBat M430 2.0 (Apr16) RMA" + ], + [ + "795", + "VCU_BXD_Nac_CIE_EtZ_0416", + "VCU BXD NAc CIE EtOH Masked ComBat M430 2.0 (Apr16) RMA Z-score" + ], + [ + "155", + "VCUEtOH_1007_R", + "VCU BXD NAc EtOH M430 2.0 (Oct07) RMA" + ], + [ + "154", + "VCUSal_1007_R", + "VCU BXD NAc EtOH vs Sal M430 2.0 (Oct07) Sscore*" + ], + [ + "409", + "VCU_NAc_Air_0113_R", + "VCU BXD NAc CIE Air M430 2.0 (Jan13) RMA" + ], + [ + "408", + "VCU_NAc_Et_0113_R", + "VCU BXD NAc CIE EtOH M430 2.0 (Jan13) RMA" + ], + [ + "407", + "VCU_NAc_AvE_0113_Ss", + "VCU BXD NAc EtOH vs CIE Air M430 2.0 (Jan13) Sscore*" ] ], "Phenotypes": [ @@ -2918,21 +3790,93 @@ "INIA Pituitary Affy MoGene 1.0ST (Jun12) RMA Exon Level" ] ], + "Popliteal Lymph Node mRNA": [ + [ + "390", + "STJ_PLN_0912", + "St Jude BXD Popliteal Lymph Node Affy HT MG-430 PM (Sep12) RMA" + ] + ], "Prefrontal Cortex mRNA": [ [ - "135", - "VCUSal_1206_R", - "VCU BXD PFC Sal M430 2.0 (Dec06) RMA" + "898", + "DOD-BXD-PFC-CD-RNA-Seq-ComB-1019", + "DOD BXD PFC GWI CD RNA-Seq ComB (Dec19) TPM Log2" + ], + [ + "899", + "DOD-BXD-PFC-CTL-RNA-Seq-ComB-1019", + "DOD BXD PFC GWI CTL RNA-Seq ComB (Dec19) TPM Log2" + ], + [ + "900", + "DOD-BXD-PFC-DFP-RNA-Seq-ComB-1019", + "DOD BXD PFC GWI DFP RNA-Seq ComB (Dec19) TPM Log2" + ], + [ + "883", + "DOD-BXD-PFC-CD-RNA-Seq-1019", + "DOD BXD PFC GWI CD RNA-Seq (Oct19) TPM Log2" + ], + [ + "884", + "DOD-BXD-PFC-CTL-RNA-Seq-1019", + "DOD BXD PFC GWI CTL RNA-Seq (Oct19) TPM Log2" + ], + [ + "885", + "DOD-BXD-PFC-DFP-RNA-Seq-1019", + "DOD BXD PFC GWI DFP RNA-Seq (Oct19) TPM Log2" + ], + [ + "135", + "VCUSal_1206_R", + "VCU BXD PFC Sal M430 2.0 (Dec06) RMA" + ], + [ + "136", + "VCUEtOH_1206_R", + "VCU BXD PFC EtOH M430 2.0 (Dec06) RMA" + ], + [ + "137", + "VCUSal_1006_R", + "VCU BXD PFC Et vs Sal M430 2.0 (Dec06) Sscore" + ], + [ + "788", + "VCU_BXD_PFC_CIE_Air_0416", + "VCU BXD PFC CIE Air Masked ComBat M430 2.0 (Apr16) RMA" + ], + [ + "789", + "VCU_BXD_PFC_CIE_AirZ_0416", + "VCU BXD PFC CIE Air Masked ComBat M430 2.0 (Apr16) RMA Z-score" + ], + [ + "790", + "VCU_BXD_PFC_CIE_Et_0416", + "VCU BXD PFC CIE EtOH Masked ComBat M430 2.0 (Apr16) RMA" ], [ - "136", - "VCUEtOH_1206_R", - "VCU BXD PFC EtOH M430 2.0 (Dec06) RMA" + "791", + "VCU_BXD_PFC_CIE_EtZ_0416", + "VCU BXD PFC CIE EtOH Masked ComBat M430 2.0 (Apr16) RMA Z-score" ], [ - "137", - "VCUSal_1006_R", - "VCU BXD PFC Et vs Sal M430 2.0 (Dec06) Sscore" + "299", + "VCU_PF_AvE_0111_Ss", + "VCU BXD PFC EtOH vs CIE Air M430 2.0 (Jan11) Sscore*" + ], + [ + "300", + "VCU_PF_Et_0111_R", + "VCU BXD PFC CIE EtOH M430 2.0 (Jan11) RMA" + ], + [ + "301", + "VCU_PF_Air_0111_R", + "VCU BXD PFC CIE Air M430 2.0 (Jan11) RMA" ] ], "Retina mRNA": [ @@ -2971,11 +3915,26 @@ "DoDTATRCRetBLMoGene2E_0316", "DoD Retina After Blast Affy MoGene 2.0 ST (Mar16) RMA Exon Level" ], + [ + "796", + "DoDRetBlastvsNormalEx_0416", + "DoD Retina Blast vs Normal Retina Affy MoGene 2.0 ST (Apr16) RMA Exon Level" + ], [ "385", "ONCRetILM6_0412", "ONC HEI Retina (April 2012) RankInv" ], + [ + "386", + "B6D2ONCILM_0412", + "B6D2 ONC Retina (April 2012) RankInv" + ], + [ + "372", + "G2HEIONCRetILM6_0911", + "G2 HEI ONC Retina Illumina V6.2 (Sep11) RankInv" + ], [ "371", "HEIONCvsCRetILM6_0911", @@ -3027,6 +3986,11 @@ "227", "IoP_SPL_RMA_0509", "IoP Affy MOE 430v2 Spleen (May09) RMA" + ], + [ + "216", + "Illum_BXD_Spl_1108", + "UWA Illumina Spleen (Nov08) RSN*" ] ], "Striatum mRNA": [ @@ -3105,6 +4069,13 @@ "HZI Treg M430v2 (Feb11) RMA" ] ], + "Thymus mRNA": [ + [ + "217", + "Illum_BXD_Thy_1108", + "UWA Illumina Thymus (Nov08) RSN*" + ] + ], "Ventral Tegmental Area mRNA": [ [ "228", @@ -3140,28 +4111,52 @@ "BXD-Harvested Genotypes" ] ], - "Hippocampus mRNA": [ + "Hippocampus Proteome": [ [ "873", "JAX-BXD-Hip-Pro-0219", "JAX BXD Hippocampal Proteome (Feb19)" ] ], + "Liver DNAm": [ + [ + "890", + "INIA-BXD-LivDNAm-1119", + "INIA BXD Liver DNAm CD-HFD (Nov19) Sesame" + ] + ], + "Liver Proteome": [ + [ + "886", + "EPFL-ETHZ-BXD-LivProtCD-HF-1119", + "EPFL/ETHZ BXD Liver Proteome CD-HFD (Nov19)" + ] + ], "Liver mRNA": [ [ "877", "UTHSC-BXD-Harv_Liv-1019", "UTHSC BXD Harvested Liver RNA-Seq (Oct19) TPM Log2" ], + [ + "850", + "UTHSC-BXD-Liv-0818", + "UTHSC BXD Liver Affy Clariom S GeneLevel Main (Aug18) RMA" + ], [ "843", "UTHSC-BXD-Harv_Liv-0118", "UTHSC BXD Harvested Liver RNA-Seq (Aug18) Log2" + ], + [ + "842", + "UTHSC-BXD-Liv-0917", + "UTHSC BXD Liver Affy Clariom S GeneLevel Main (Sep17) RMA" ] ], "Phenotypes": [ [ - "None", + "660", "BXD-HarvestedPublish", "BXD-NIA-Longevity Phenotypes" ] @@ -3263,6 +4258,29 @@ ] ] }, + "CC": { + "Genotypes": [ + [ + "663", + "CCGeno", + "CC Genotypes" + ] + ], + "Midbrain mRNA": [ + [ + "894", + "LSRU-CC-ST-1219", + "LSRU CC Male Midbrain RNA-Seq (Dec19) TPM Log2" + ] + ], + "Phenotypes": [ + [ + "662", + "CCPublish", + "CC Phenotypes" + ] + ] + }, "CFW": { "Hippocampus mRNA": [ [ @@ -3360,9 +4378,35 @@ "CIE-RMAPublish", "CIE-RMA Phenotypes" ] + ], + "Prefrontal Cortex mRNA": [ + [ + "832", + "INIA_UTHSC_PFC_AffyMTA1_May17", + "INIA-UTHSC Prefrontal Cortex CIE Affy MTA 1.0 GeneLevel (Apr17) RMA" + ] + ], + "Striatum mRNA": [ + [ + "833", + "INIA_UTHSC_Str_AffyMTA1_May17", + "INIA-UTHSC Striatum CIE Affy MTA 1.0 GeneLevel (Apr17) RMA" + ] ] }, "CMS": { + "Hippocampus mRNA": [ + [ + "771", + "CMS_Hipp1115", + "Hippocampus Mouse Transcriptome Assay 1.0 Gene Level Main (Nov15) RMA" + ], + [ + "800", + "CMS_Hipp_ZScr_1115", + "Hippocampus Mouse Transcriptome Assay 1.0 Gene Level Z-Score (Nov15) RMA" + ] + ], "Phenotypes": [ [ "None", @@ -3520,6 +4564,92 @@ ] ] }, + "DOD-BXD-GWI": { + "Genotypes": [ + [ + "None", + "DOD-BXD-GWIGeno", + "DOD-BXD-GWI Genotypes" + ] + ], + "Prefrontal Cortex mRNA": [ + [ + "895", + "DOD-BXD-Ind-PFC-CD-RNA-Seq-ComB-1019", + "DOD BXD INDV PFC GWI CD RNA-Seq ComB (Dec19) TPM Log2" + ], + [ + "896", + "DOD-BXD-Ind-PFC-CTL-RNA-Seq-ComB-1019", + "DOD BXD INDV PFC GWI CTL RNA-Seq ComB (Dec19) TPM Log2" + ], + [ + "897", + "DOD-BXD-Ind-PFC-DFP-RNA-Seq-ComB-1019", + "DOD BXD INDV PFC GWI DFP RNA-Seq ComB (Dec19) TPM Log2" + ], + [ + "880", + "DOD-BXD-Ind-PFC-CD-RNA-Seq-1019", + "DOD BXD INDV PFC GWI CD RNA-Seq (Oct19) TPM Log2" + ], + [ + "881", + "DOD-BXD-Ind-PFC-CTL-RNA-Seq-1019", + "DOD BXD INDV PFC GWI CTL RNA-Seq (Oct19) TPM Log2" + ], + [ + "882", + "DOD-BXD-Ind-PFC-DFP-RNA-Seq-1019", + "DOD BXD INDV PFC GWI DFP RNA-Seq (Oct19) TPM Log2" + ] + ] + }, + "EMSR": { + "Hippocampus mRNA": [ + [ + "825", + "UTHSC_EMSR_All_AffyMTA1_Mar17", + "UTHSC Hippocampus All Treatments Affy MTA 1.0 Gene Level (Mar17) RMA" + ], + [ + "826", + "UTHSC_EMSR_Sal_AffyMTA1_Mar17", + "UTHSC Hippocampus Saline Affy MTA 1.0 Gene Level (Mar17) RMA" + ], + [ + "827", + "UTHSC_EMSR_Et_AffyMTA1_Mar17", + "UTHSC Hippocampus Ethanol Affy MTA 1.0 Gene Level (Mar17) RMA" + ], + [ + "828", + "UTHSC_EMSR_St_AffyMTA1_Mar17", + "UTHSC Hippocampus Stress Affy MTA 1.0 Gene Level (Mar17) RMA" + ], + [ + "829", + "UTHSC_EMSR_EtSt_AffyMTA1_Mar17", + "UTHSC Hippocampus Ethanol-Stress Affy MTA 1.0 Gene Level (Mar17) RMA" + ] + ] + }, + "HET3-ITP": { + "Genotypes": [ + [ + "None", + "HET3-ITPGeno", + "HET3-ITP Genotypes" + ] + ], + "Phenotypes": [ + [ + "661", + "HET3-ITPPublish", + "HET3 ITP Longevity Phenotypes" + ] + ] + }, "HS": { "Hippocampus mRNA": [ [ @@ -3559,16 +4689,123 @@ ] ] }, - "LGSM-AIG34_50-56-GBS": { + "JAX-D2-Mono-RNA-Seq": { + "Retina mRNA": [ + [ + "878", + "JAX-D2-Mono1vPBMC-Ret-RNA-Seq-0619", + "JAX DBA/2J Monocyte 1 vs PBMC RNA-Seq (Jun19)" + ], + [ + "879", + "JAX-D2-Mono2vPBMC-Ret-RNA-Seq-0619", + "JAX DBA/2J Monocyte 2 vs PBMC RNA-Seq (Jun19)" + ] + ] + }, + "LGSM-AI": { + "Hippocampus mRNA": [ + [ + "874", + "UCSD_AIL_HIP_RNA-Seq_log2_0418", + "UCSD AIL Hippocampus (Apr18) RNA-Seq Log2" + ], + [ + "844", + "UCSD_AIL_HIP_RNA-Seq_0418", + "UCSD AIL Hippocampus (Apr18) RNA-Seq" + ] + ], "Phenotypes": [ [ "None", + "LGSM-AIPublish", + "LGSM AI Phenotypes" + ] + ], + "Prefrontal Cortex mRNA": [ + [ + "876", + "UCSD_AIL_PFC_RNA-Seq_log2_0418", + "UCSD AIL Prefrontal Cortex (Apr18) RNA-Seq Log2" + ], + [ + "846", + "UCSD_AIL_PFC_RNA-Seq_0418", + "UCSD AIL Prefrontal Cortex (Apr18) RNA-Seq" + ] + ], + "Striatum mRNA": [ + [ + "875", + "UCSD_AIL_STR_RNA-Seq_log2_0418", + "UCSD AIL Striatum (Apr18) RNA-Seq Log2" + ], + [ + "845", + "UCSD_AIL_STR_RNA-Seq_0418", + "UCSD AIL Striatum (Apr18) RNA-Seq" + ] + ] + }, + "LGSM-AI-G34-A": { + "Phenotypes": [ + [ + "655", + "LGSM-AI-G34-APublish", + "LGSM AI G34 Phenotypes" + ] + ] + }, + "LGSM-AI-G34-GBS": { + "Phenotypes": [ + [ + "656", + "LGSM-AI-G34-GBSPublish", + "LGSM AI G34 GBS Phenotypes" + ] + ] + }, + "LGSM-AI-G34_39-43-GBS": { + "Phenotypes": [ + [ + "657", + "LGSM-AI-G34_39-43-GBSPublish", + "LGSM AI G34 G39-43 GBS Phenotypes" + ] + ] + }, + "LGSM-AI-G39-43-GBS": { + "Phenotypes": [ + [ + "654", + "LGSM-AI-G39-43-GBSPublish", + "LGSM AI G39-43 GBS Phenotypes" + ] + ] + }, + "LGSM-AIG34_50-56-GBS": { + "Phenotypes": [ + [ + "659", "LGSM-AIG34_50-56-GBSPublish", - "LGSM AIG34/50-56 GBS Phenotypes" + "LGSM AI G34/50-56 GBS Phenotypes" ] ] }, "LXS": { + "Brain mRNA": [ + [ + "783", + "UCAMC_LXSBrEtOH_RNA-Seq_0216", + "UCAMC LXS Whole Brain Ethanol RNA Sequence (Feb16) FPKM*" + ], + [ + "784", + "UCAMC_LXSBrSal_RNA-Seq_0216", + "UCAMC LXS Whole Brain Saline RNA Sequence (Feb16) FPKM*" + ] + ], "Genotypes": [ [ "601", @@ -3577,6 +4814,11 @@ ] ], "Hippocampus mRNA": [ + [ + "214", + "Illum_LXS_Hipp_NOE_1008", + "Hippocampus Illumina NOE (Oct08) RankInv beta" + ], [ "211", "Illum_LXS_Hipp_RSS_1008", @@ -3597,11 +4839,6 @@ "Illum_LXS_Hipp_RSE_1008", "Hippocampus Illumina RSE (Oct08) RankInv beta" ], - [ - "214", - "Illum_LXS_Hipp_NOE_1008", - "Hippocampus Illumina NOE (Oct08) RankInv beta" - ], [ "143", "Illum_LXS_Hipp_loess0807", @@ -3650,6 +4887,16 @@ "130", "VCUSal_0806_R", "VCU LXS PFC Sal M430A 2.0 (Aug06) RMA" + ], + [ + "132", + "VCUEt_vs_Sal_0806_R", + "VCU LXS PFC Et vs Sal M430A 2.0 (Aug06) Sscore*" + ], + [ + "131", + "VCUEtOH_0806_R", + "VCU LXS PFC EtOH M430A 2.0 (Aug06) RMA" ] ] }, @@ -3701,6 +4948,11 @@ "273", "UMUTAffyExon_0209_RMA_MDP", "UMUTAffy Hippocampus Exon (Feb09) RMA MDP" + ], + [ + "594", + "UFL-MDP-Hipp0814", + "UFL MDP Hippocampus Antidepressant Affy Mouse 430 2.0 (Aug14) RMA" ] ], "Liver mRNA": [ @@ -3795,6 +5047,36 @@ "SOTNOT-OHSU Genotypes" ] ] + }, + "Scripps-2013": { + "Anterior Cingulate Cortex mRNA": [ + [ + "450", + "ScrBXDACC4G0513", + "Scripps BXD ACC 4 Groups Affy Mouse Gene 1.0 ST (May13) RMA Gene Level" + ], + [ + "451", + "ScrBXDACC4GEx0513", + "Scripps BXD ACC 4 Groups Affy Mouse Gene 1.0 ST (May13) RMA Exon Level" + ] + ] + }, + "UTHSC-Cannabinoid": { + "Genotypes": [ + [ + "None", + "UTHSC-CannabinoidGeno", + "UTHSC-Cannabinoid Genotypes" + ] + ], + "Phenotypes": [ + [ + "None", + "UTHSC-CannabinoidPublish", + "UTHSC Cannabinoid Pilot Phenotypes" + ] + ] } }, "poplar": { @@ -3809,22 +5091,6 @@ } }, "rat": { - "HRDP": { - "Genotypes": [ - [ - "None", - "HRDPGeno", - "HRDP Genotypes" - ] - ], - "Phenotypes": [ - [ - "None", - "HRDPPublish", - "HRDP Phenotypes" - ] - ] - }, "HSNIH-Palmer": { "Infralimbic Cortex mRNA": [ [ @@ -4011,295 +5277,404 @@ "arabidopsis": [ [ "BayXSha", - "BayXSha" + "BayXSha", + "Family:None" ], [ "ColXBur", - "ColXBur" + "ColXBur", + "Family:None" ], [ "ColXCvi", - "ColXCvi" + "ColXCvi", + "Family:None" ] ], "barley": [ [ "QSM", - "QSM" + "QSM", + "Family:None" ], [ "SXM", - "SXM" + "SXM", + "Family:None" ] ], "drosophila": [ [ "DGRP", - "Drosophila Genetic Reference Panel" + "Drosophila Genetic Reference Panel", + "Family:None" ], [ "Oregon-R_x_2b3", - "Oregon-R x 2b3" + "Oregon-R x 2b3", + "Family:None" ] ], "human": [ [ "HB", - "Brain, Aging: AD, HD, Normal Gene Expression (Harvard/Merck)" + "Brain, Aging: AD, HD, Normal Gene Expression (Harvard/Merck)", + "Family:None" ], [ "AD-cases-controls", - "Brain, Aging: AD, Normal Gene Expression (Liang)" + "Brain, Aging: AD, Normal Gene Expression (Liang)", + "Family:None" ], [ "AD-cases-controls-Myers", - "Brain, Aging: AD, Normal Gene Expression with Genotypes (Myers)" + "Brain, Aging: AD, Normal Gene Expression with Genotypes (Myers)", + "Family:None" ], [ "Aging-Brain-UCI", - "Brain, Aging: Normal Gene Expression (UCI/Cotman)" + "Brain, Aging: Normal Gene Expression (UCI/Cotman)", + "Family:None" ], [ "HCP", - "Brain, Cognition, Human Connectome Project" + "Brain, Cognition, Human Connectome Project", + "Family:None" ], [ "HSB", - "Brain, Development: Normal Gene Expression (Yale/Sestan)" + "Brain, Development: Normal Gene Expression (Yale/Sestan)", + "Family:None" ], [ "Brain-Normal-NIH-Gibbs", - "Brain: Normal Gene Expression (NIH/Gibbs)" + "Brain: Normal Gene Expression (NIH/Gibbs)", + "Family:None" ], [ "CANDLE", - "Child Development: CANDLE Cohort with Genotypes (TUCI/UTHSC)" + "Child Development: CANDLE Cohort with Genotypes (TUCI/UTHSC)", + "Family:None" ], [ "GTEx", - "GTEx v3 All Tissues, RNA-Seq with Genotypes" + "GTEx v3 All Tissues, RNA-Seq with Genotypes", + "Family:None" ], [ "GTEx_v5", - "GTEx v5 All Tissues, RNA-Seq with Genotypes" + "GTEx v5 All Tissues, RNA-Seq with Genotypes", + "Family:None" + ], + [ + "GTEx_v8", + "GTEx v8 All Tissues, RNA-Seq without Genotypes", + "Family:None" ], [ "HLC", - "Liver: Normal Gene Expression with Genotypes (Merck)" + "Liver: Normal Gene Expression with Genotypes (Merck)", + "Family:None" ], [ "HLT", - "Lung: Normal Gene Expression (Merck)" + "Lung: Normal Gene Expression (Merck)", + "Family:None" ], [ "CEPH-2004", - "Lymphoblastoid Cells: Gene Expression (CEPH, Williams)" + "Lymphoblastoid Cells: Gene Expression (CEPH, Williams)", + "Family:None" ], [ "Islets-Gerling", - "Pancreatic: Islets (UTHSC/Gerling)" + "Pancreatic: Islets (UTHSC/Gerling)", + "Family:None" ], [ "TIGEM-Retina-RNA-Seq", - "Retina: Normal Adult Gene Expression, RNA-Seq (TIGEM)" + "Retina: Normal Adult Gene Expression, RNA-Seq (TIGEM)", + "Family:None" ] ], "mouse": [ [ - "AIL", - "AIL Advanced Intercross Line" + "AKXD", + "AKXD Family", + "Family:Reference Populations" + ], + [ + "AXBXA", + "AXB/BXA Family", + "Family:Reference Populations" + ], + [ + "BXD", + "BXD Family", + "Family:Reference Populations" + ], + [ + "BXH", + "BXH Family", + "Family:Reference Populations" + ], + [ + "CC", + "CC Family", + "Family:Reference Populations" + ], + [ + "CXB", + "CXB Family", + "Family:Reference Populations" + ], + [ + "LXS", + "ILSXISS (LXS) Family", + "Family:Reference Populations" ], [ - "AIL-LGSM-F34-A", - "AIL LGSM F34 (Array)" + "MDP", + "Mouse Diversity Panel", + "Family:Reference Populations" ], [ - "AIL-LGSM-F34-GBS", - "AIL LGSM F34 (GBS)" + "B6D2RI", + "BXD Aged Hippocampus", + "Family:BXD Individual Data" ], [ - "AIL-LGSM-F34-F39-43-GBS", - "AIL LGSM F34 and F39-43 (GBS)" + "BXD-Bone", + "BXD Bone Individual Data", + "Family:BXD Individual Data" ], [ - "AIL-LGSM-F39-43-GBS", - "AIL LGSM F39-43 (GBS)" + "DOD-BXD-GWI", + "BXD DOD Gulf War Illness", + "Family:BXD Individual Data" ], [ - "AKXD", - "AKXD RI Family" + "BXD-Harvested", + "BXD NIA Longevity Study", + "Family:BXD Individual Data" ], [ - "AXBXA", - "AXB/BXA RI Family" + "UTHSC-Cannabinoid", + "BXD UTHSC Cannabinoid Pilot", + "Family:BXD Individual Data" ], [ "B6BTBRF2", - "B6BTBRF2" + "B6BTBRF2", + "Family:Crosses, AIL, HS" ], [ - "Linsenbardt-Boehm", - "B6D2 EtOH Selected Advanced Intercross" + "BHHBF2", + "B6C3HF2 UCLA Metabolism", + "Family:Crosses, AIL, HS" ], [ - "B6D2F2", - "B6D2F2" + "BHF2", + "B6C3HF2(APOE-) UCLA Metabolism", + "Family:Crosses, AIL, HS" ], [ - "B6D2F2-PSU", - "B6D2F2 PSU" + "Linsenbardt-Boehm", + "B6D2 EtOH Selected Advanced Intercross", + "Family:Crosses, AIL, HS" ], [ - "BDF2-1999", - "BDF2 UCLA" + "B6D2F2", + "B6D2F2 OHSU Brain", + "Family:Crosses, AIL, HS" ], [ "BDF2-2005", - "BDF2-2005" + "B6D2F2 OHSU Striatum", + "Family:Crosses, AIL, HS" ], [ - "BHHBF2", - "BH/HB F2 UCLA" + "B6D2F2-PSU", + "B6D2F2 PSU Muscle", + "Family:Crosses, AIL, HS" ], [ - "BHF2", - "BHF2 (Apoe Null) UCLA" + "BDF2-1999", + "B6D2F2 UCLA Liver", + "Family:Crosses, AIL, HS" ], [ - "B6D2RI", - "BXD Aged" + "CTB6F2", + "CastB6/B6Cast F2 UCLA", + "Family:Crosses, AIL, HS" ], [ - "BXD-Bone", - "BXD Bone Individual Data" + "CFW", + "CFW Outbred GWAS", + "Family:Crosses, AIL, HS" ], [ - "BXD-Harvested", - "BXD NIA Longevity Study" + "HET3-ITP", + "HET3 ITP Longevity", + "Family:Crosses, AIL, HS" ], [ - "BXD", - "BXD RI Family" + "HS", + "Heterogeneous Stock", + "Family:Crosses, AIL, HS" ], [ - "BXD300", - "BXD300" + "HS-CC", + "Heterogeneous Stock Collaborative Cross", + "Family:Crosses, AIL, HS" ], [ - "BXH", - "BXH RI Family" + "LGSM-AI-G34_39-43-GBS", + "LGSM AI G34 G39-43 Palmer (GBS)", + "Family:Crosses, AIL, HS" ], [ - "CTB6F2", - "CastB6/B6Cast F2 UCLA" + "LGSM-AI-G34-A", + "LGSM AI G34 Palmer (Array)", + "Family:Crosses, AIL, HS" ], [ - "CFW", - "CFW Outbred GWAS" + "LGSM-AI-G34-GBS", + "LGSM AI G34 Palmer (GBS)", + "Family:Crosses, AIL, HS" ], [ - "CIE-INIA", - "Chronic Intermittent Ethanol Phase 1" + "LGSM-AIG34_50-56-GBS", + "LGSM AI G34/50-56 Lionikas (GBS)", + "Family:Crosses, AIL, HS" ], [ - "CIE-RMA", - "Chronic Intermittent Ethanol Phase 2" + "LGSM-AI-G39-43-GBS", + "LGSM AI G39-43 Palmer (GBS)", + "Family:Crosses, AIL, HS" ], [ - "CMS", - "Chronic Mild Stress" + "LGSM-AI", + "LGSM AI Palmer", + "Family:Crosses, AIL, HS" ], [ - "CXB", - "CXB RI Family (strain means)" + "SOTNOT-OHSU", + "SOTNOT-OHSU", + "Family:Crosses, AIL, HS" ], [ - "D2GM", - "D2 Glaucoma Model" + "B6-Lens", + "B6 Lens", + "Family:Non-genetic Cohort" ], [ - "B6D2", - "Glaucoma and Aged Retina, UTHSC" + "CIE-INIA", + "Chronic Intermittent Ethanol Phase 1", + "Family:Non-genetic Cohort" ], [ - "HS", - "Heterogeneous Stock" + "CIE-RMA", + "Chronic Intermittent Ethanol Phase 2", + "Family:Non-genetic Cohort" ], [ - "HS-CC", - "Heterogeneous Stock Collaborative Cross" + "CMS", + "Chronic Mild Stress", + "Family:Non-genetic Cohort" ], [ - "LXS", - "ILSXISS (LXS) RI Family (strain means)" + "D2GM", + "D2 Glaucoma Model", + "Family:Non-genetic Cohort" ], [ - "LGSM-AIG34_50-56-GBS", - "LGSM AI G34/50-56 Lionikas (GBS)" + "JAX-D2-Mono-RNA-Seq", + "D2 Glaucoma Monocyte JAX", + "Family:Non-genetic Cohort" ], [ - "MDP", - "Mouse Diversity Panel (strain means)" + "EMSR", + "Ethanol-Medicated Stress Reduction", + "Family:Non-genetic Cohort" + ], + [ + "B6D2", + "Glaucoma and Aged Retina UTHSC", + "Family:Non-genetic Cohort" ], [ "NZBXFVB-N2", - "NZB/FVB N2 NCI" + "NZB/FVB N2 NCI", + "Family:Non-genetic Cohort" ], [ "C57BL-6JxC57BL-6NJF2", - "Reduced Complexity Cross (B6JxB6N F2)" + "Reduced Complexity Cross (B6JxB6N F2)", + "Family:Non-genetic Cohort" ], [ "Retina-RGC-Rheaume", - "Retina RGC Rheaume" + "Retina RGC Rheaume", + "Family:Non-genetic Cohort" ], [ - "SOTNOT-OHSU", - "SOTNOT-OHSU" + "Scripps-2013", + "Scripps C57BL/6J", + "Family:Non-genetic Cohort" + ], + [ + "BXD300", + "BXD300", + "Family:None" ] ], "poplar": [ [ "Poplar", - "Poplar" + "Poplar", + "Family:None" ] ], "rat": [ [ "HXBBXH", - "HXB/BXH" - ], - [ - "HRDP", - "Hybrid Rat Diversity Panel" + "Hybrid Rat Diversity Panel (Includes HXB/BXH)", + "Family:None" ], [ "HSNIH-Palmer", - "NIH Heterogeneous Stock (Palmer)" + "NIH Heterogeneous Stock (Palmer)", + "Family:None" ], [ "HSNIH-RGSMC", - "NIH Heterogeneous Stock (RGSMC 2013)" + "NIH Heterogeneous Stock (RGSMC 2013)", + "Family:None" ], [ "SRxSHRSPF2", - "UIOWA SRxSHRSP F2" + "UIOWA SRxSHRSP F2", + "Family:None" ] ], "soybean": [ [ "J12XJ58F11", - "J12XJ58F11" + "J12XJ58F11", + "Family:None" ], [ "J12XJ58F2", - "J12XJ58F2" + "J12XJ58F2", + "Family:None" ] ], "tomato": [ [ "LXP", - "LXP" + "LXP", + "Family:None" ] ] }, @@ -4480,6 +5855,10 @@ "Phenotypes", "Phenotypes" ], + [ + "Methylation", + "Methylation" + ], [ "Newborn Cord Blood mRNA", "Newborn Cord Blood mRNA" @@ -4493,12 +5872,206 @@ ], "GTEx": [ [ - "Adipose tissue, subcutaneous mRNA", - "Adipose tissue, subcutaneous mRNA" + "Adipose Tissue, Subcutaneous mRNA", + "Adipose Tissue, Subcutaneous mRNA" + ], + [ + "Adipose Tissue, Visceral mRNA", + "Adipose Tissue, Visceral mRNA" + ], + [ + "Adrenal Gland mRNA", + "Adrenal Gland mRNA" + ], + [ + "Amygdala mRNA", + "Amygdala mRNA" + ], + [ + "Anterior Cingulate Cortex mRNA", + "Anterior Cingulate Cortex mRNA" + ], + [ + "Aorta mRNA", + "Aorta mRNA" + ], + [ + "Blood, Cells - EBV-Transformed Lymphocytes mRNA", + "Blood, Cells - EBV-Transformed Lymphocytes mRNA" + ], + [ + "Breast - Mammary Tissue mRNA", + "Breast - Mammary Tissue mRNA" + ], + [ + "Caudate mRNA", + "Caudate mRNA" + ], + [ + "Cells - EBV-Transformed Lymphocytes mRNA", + "Cells - EBV-Transformed Lymphocytes mRNA" + ], + [ + "Cells - Leukemia Cell Line (CML) mRNA", + "Cells - Leukemia Cell Line (CML) mRNA" + ], + [ + "Cells - Transformed Fibroblasts mRNA", + "Cells - Transformed Fibroblasts mRNA" + ], + [ + "Cerebellar Cortex mRNA", + "Cerebellar Cortex mRNA" + ], + [ + "Cerebellar Hemisphere mRNA", + "Cerebellar Hemisphere mRNA" + ], + [ + "Cerebellum mRNA", + "Cerebellum mRNA" + ], + [ + "Colon - Transverse mRNA", + "Colon - Transverse mRNA" + ], + [ + "Coronary mRNA", + "Coronary mRNA" + ], + [ + "Esophagus - Mucosa mRNA", + "Esophagus - Mucosa mRNA" + ], + [ + "Esophagus - Muscularis mRNA", + "Esophagus - Muscularis mRNA" + ], + [ + "Fallopian Tube mRNA", + "Fallopian Tube mRNA" + ], + [ + "Frontal Cortex mRNA", + "Frontal Cortex mRNA" + ], + [ + "Heart - Atrial Appendage mRNA", + "Heart - Atrial Appendage mRNA" + ], + [ + "Heart - Left Ventricle mRNA", + "Heart - Left Ventricle mRNA" + ], + [ + "Hippocampus mRNA", + "Hippocampus mRNA" + ], + [ + "Hypothalamus mRNA", + "Hypothalamus mRNA" + ], + [ + "Kidney mRNA", + "Kidney mRNA" + ], + [ + "Liver mRNA", + "Liver mRNA" + ], + [ + "Lung mRNA", + "Lung mRNA" + ], + [ + "Muscle mRNA", + "Muscle mRNA" + ], + [ + "Nerve - Tibial mRNA", + "Nerve - Tibial mRNA" + ], + [ + "Nucleus Accumbens mRNA", + "Nucleus Accumbens mRNA" + ], + [ + "Ovary mRNA", + "Ovary mRNA" + ], + [ + "Pancreas mRNA", + "Pancreas mRNA" + ], + [ + "Pituitary Gland mRNA", + "Pituitary Gland mRNA" + ], + [ + "Prostate mRNA", + "Prostate mRNA" + ], + [ + "Putamen mRNA", + "Putamen mRNA" + ], + [ + "Skin - Not Sun Exposed (Suprapubic) mRNA", + "Skin - Not Sun Exposed (Suprapubic) mRNA" + ], + [ + "Skin - Sun Exposed (Lower leg) mRNA", + "Skin - Sun Exposed (Lower leg) mRNA" + ], + [ + "Spinal Cord mRNA", + "Spinal Cord mRNA" + ], + [ + "Stomach mRNA", + "Stomach mRNA" + ], + [ + "Substantia Nigra mRNA", + "Substantia Nigra mRNA" + ], + [ + "Testis mRNA", + "Testis mRNA" + ], + [ + "Thyroid mRNA", + "Thyroid mRNA" + ], + [ + "Tibial mRNA", + "Tibial mRNA" + ], + [ + "Uterus mRNA", + "Uterus mRNA" + ], + [ + "Vagina mRNA", + "Vagina mRNA" + ], + [ + "Whole Blood mRNA", + "Whole Blood mRNA" + ] + ], + "GTEx_v5": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Adipose Tissue, Subcutaneous mRNA", + "Adipose Tissue, Subcutaneous mRNA" ], [ - "Adipose tissue, visceral mRNA", - "Adipose tissue, visceral mRNA" + "Adipose Tissue, Visceral mRNA", + "Adipose Tissue, Visceral mRNA" ], [ "Adrenal Gland mRNA", @@ -4517,8 +6090,12 @@ "Aorta mRNA" ], [ - "Blood, Cells - EBV-Transformed Lymphocytes mRNA", - "Blood, Cells - EBV-Transformed Lymphocytes mRNA" + "Bladder mRNA", + "Bladder mRNA" + ], + [ + "Bone Marrow mRNA", + "Bone Marrow mRNA" ], [ "Breast - Mammary Tissue mRNA", @@ -4532,10 +6109,6 @@ "Cells - EBV-Transformed Lymphocytes mRNA", "Cells - EBV-Transformed Lymphocytes mRNA" ], - [ - "Cells - Leukemia Cell Line (CML) mRNA", - "Cells - Leukemia Cell Line (CML) mRNA" - ], [ "Cells - Transformed Fibroblasts mRNA", "Cells - Transformed Fibroblasts mRNA" @@ -4552,6 +6125,14 @@ "Cerebellum mRNA", "Cerebellum mRNA" ], + [ + "Cervix mRNA", + "Cervix mRNA" + ], + [ + "Colon - Sigmoid mRNA", + "Colon - Sigmoid mRNA" + ], [ "Colon - Transverse mRNA", "Colon - Transverse mRNA" @@ -4560,6 +6141,10 @@ "Coronary mRNA", "Coronary mRNA" ], + [ + "Esophagus - Gastroesophageal mRNA", + "Esophagus - Gastroesophageal mRNA" + ], [ "Esophagus - Mucosa mRNA", "Esophagus - Mucosa mRNA" @@ -4636,6 +6221,10 @@ "Putamen mRNA", "Putamen mRNA" ], + [ + "Salivary Gland mRNA", + "Salivary Gland mRNA" + ], [ "Skin - Not Sun Exposed (Suprapubic) mRNA", "Skin - Not Sun Exposed (Suprapubic) mRNA" @@ -4644,10 +6233,18 @@ "Skin - Sun Exposed (Lower leg) mRNA", "Skin - Sun Exposed (Lower leg) mRNA" ], + [ + "Small Intestine - Terminal Ileum mRNA", + "Small Intestine - Terminal Ileum mRNA" + ], [ "Spinal Cord mRNA", "Spinal Cord mRNA" ], + [ + "Spleen mRNA", + "Spleen mRNA" + ], [ "Stomach mRNA", "Stomach mRNA" @@ -4681,18 +6278,18 @@ "Whole Blood mRNA" ] ], - "GTEx_v5": [ + "GTEx_v8": [ [ "Phenotypes", "Phenotypes" ], [ - "Adipose tissue, subcutaneous mRNA", - "Adipose tissue, subcutaneous mRNA" + "Adipose Tissue, Subcutaneous mRNA", + "Adipose Tissue, Subcutaneous mRNA" ], [ - "Adipose tissue, visceral mRNA", - "Adipose tissue, visceral mRNA" + "Adipose Tissue, Visceral mRNA", + "Adipose Tissue, Visceral mRNA" ], [ "Adrenal Gland mRNA", @@ -4710,14 +6307,6 @@ "Aorta mRNA", "Aorta mRNA" ], - [ - "Bladder mRNA", - "Bladder mRNA" - ], - [ - "Bone Marrow mRNA", - "Bone Marrow mRNA" - ], [ "Breast - Mammary Tissue mRNA", "Breast - Mammary Tissue mRNA" @@ -4746,10 +6335,6 @@ "Cerebellum mRNA", "Cerebellum mRNA" ], - [ - "Cervix mRNA", - "Cervix mRNA" - ], [ "Colon - Sigmoid mRNA", "Colon - Sigmoid mRNA" @@ -4774,10 +6359,6 @@ "Esophagus - Muscularis mRNA", "Esophagus - Muscularis mRNA" ], - [ - "Fallopian Tube mRNA", - "Fallopian Tube mRNA" - ], [ "Frontal Cortex mRNA", "Frontal Cortex mRNA" @@ -5009,6 +6590,10 @@ [ "Phenotypes", "Phenotypes" + ], + [ + "Islets mRNA", + "Islets mRNA" ] ], "TIGEM-Retina-RNA-Seq": [ @@ -5023,52 +6608,6 @@ ] }, "mouse": { - "AIL": [ - [ - "Phenotypes", - "Phenotypes" - ], - [ - "Genotypes", - "Genotypes" - ], - [ - "Hippocampus mRNA", - "Hippocampus mRNA" - ], - [ - "Prefrontal Cortex mRNA", - "Prefrontal Cortex mRNA" - ], - [ - "Striatum mRNA", - "Striatum mRNA" - ] - ], - "AIL-LGSM-F34-A": [ - [ - "Phenotypes", - "Phenotypes" - ] - ], - "AIL-LGSM-F34-F39-43-GBS": [ - [ - "Phenotypes", - "Phenotypes" - ] - ], - "AIL-LGSM-F34-GBS": [ - [ - "Phenotypes", - "Phenotypes" - ] - ], - "AIL-LGSM-F39-43-GBS": [ - [ - "Phenotypes", - "Phenotypes" - ] - ], "AKXD": [ [ "Genotypes", @@ -5105,6 +6644,16 @@ "Liver mRNA" ] ], + "B6-Lens": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Ocular Lens mRNA", + "Ocular Lens mRNA" + ] + ], "B6BTBRF2": [ [ "Phenotypes", @@ -5123,6 +6672,14 @@ [ "Phenotypes", "Phenotypes" + ], + [ + "Retina microRNA", + "Retina microRNA" + ], + [ + "Retina mRNA", + "Retina mRNA" ] ], "B6D2F2": [ @@ -5143,6 +6700,10 @@ [ "Genotypes", "Genotypes" + ], + [ + "Muscle mRNA", + "Muscle mRNA" ] ], "B6D2RI": [ @@ -5195,6 +6756,10 @@ [ "Liver mRNA", "Liver mRNA" + ], + [ + "Muscle mRNA", + "Muscle mRNA" ] ], "BHHBF2": [ @@ -5284,6 +6849,10 @@ "Hippocampal Precursor Cells mRNA", "Hippocampal Precursor Cells mRNA" ], + [ + "Hippocampus microRNA", + "Hippocampus microRNA" + ], [ "Hippocampus mRNA", "Hippocampus mRNA" @@ -5296,6 +6865,14 @@ "Kidney mRNA", "Kidney mRNA" ], + [ + "Leucocytes mRNA", + "Leucocytes mRNA" + ], + [ + "Liver DNAm", + "Liver DNAm" + ], [ "Liver Metabolome", "Liver Metabolome" @@ -5316,6 +6893,10 @@ "Midbrain mRNA", "Midbrain mRNA" ], + [ + "Muscle Metabolome", + "Muscle Metabolome" + ], [ "Muscle mRNA", "Muscle mRNA" @@ -5324,6 +6905,10 @@ "Neocortex mRNA", "Neocortex mRNA" ], + [ + "Neutrophils mRNA", + "Neutrophils mRNA" + ], [ "Nucleus Accumbens mRNA", "Nucleus Accumbens mRNA" @@ -5332,6 +6917,10 @@ "Pituitary Gland mRNA", "Pituitary Gland mRNA" ], + [ + "Popliteal Lymph Node mRNA", + "Popliteal Lymph Node mRNA" + ], [ "Prefrontal Cortex mRNA", "Prefrontal Cortex mRNA" @@ -5356,6 +6945,10 @@ "T Cell (regulatory) mRNA", "T Cell (regulatory) mRNA" ], + [ + "Thymus mRNA", + "Thymus mRNA" + ], [ "Ventral Tegmental Area mRNA", "Ventral Tegmental Area mRNA" @@ -5377,12 +6970,20 @@ "Genotypes" ], [ - "Hippocampus mRNA", - "Hippocampus mRNA" + "Hippocampus Proteome", + "Hippocampus Proteome" + ], + [ + "Liver DNAm", + "Liver DNAm" ], [ "Liver mRNA", "Liver mRNA" + ], + [ + "Liver Proteome", + "Liver Proteome" ] ], "BXD300": [ @@ -5431,6 +7032,20 @@ "Genotypes" ] ], + "CC": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Genotypes", + "Genotypes" + ], + [ + "Midbrain mRNA", + "Midbrain mRNA" + ] + ], "CFW": [ [ "Phenotypes", @@ -5471,12 +7086,24 @@ [ "Midbrain mRNA", "Midbrain mRNA" + ], + [ + "Prefrontal Cortex mRNA", + "Prefrontal Cortex mRNA" + ], + [ + "Striatum mRNA", + "Striatum mRNA" ] ], "CMS": [ [ "Phenotypes", "Phenotypes" + ], + [ + "Hippocampus mRNA", + "Hippocampus mRNA" ] ], "CTB6F2": [ @@ -5541,6 +7168,32 @@ "Retina mRNA" ] ], + "DOD-BXD-GWI": [ + [ + "Genotypes", + "Genotypes" + ], + [ + "Prefrontal Cortex mRNA", + "Prefrontal Cortex mRNA" + ] + ], + "EMSR": [ + [ + "Hippocampus mRNA", + "Hippocampus mRNA" + ] + ], + "HET3-ITP": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Genotypes", + "Genotypes" + ] + ], "HS": [ [ "Phenotypes", @@ -5565,6 +7218,54 @@ "Striatum mRNA" ] ], + "JAX-D2-Mono-RNA-Seq": [ + [ + "Retina mRNA", + "Retina mRNA" + ] + ], + "LGSM-AI": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Hippocampus mRNA", + "Hippocampus mRNA" + ], + [ + "Prefrontal Cortex mRNA", + "Prefrontal Cortex mRNA" + ], + [ + "Striatum mRNA", + "Striatum mRNA" + ] + ], + "LGSM-AI-G34-A": [ + [ + "Phenotypes", + "Phenotypes" + ] + ], + "LGSM-AI-G34-GBS": [ + [ + "Phenotypes", + "Phenotypes" + ] + ], + "LGSM-AI-G34_39-43-GBS": [ + [ + "Phenotypes", + "Phenotypes" + ] + ], + "LGSM-AI-G39-43-GBS": [ + [ + "Phenotypes", + "Phenotypes" + ] + ], "LGSM-AIG34_50-56-GBS": [ [ "Phenotypes", @@ -5580,6 +7281,10 @@ "Genotypes", "Genotypes" ], + [ + "Brain mRNA", + "Brain mRNA" + ], [ "Hippocampus mRNA", "Hippocampus mRNA" @@ -5654,6 +7359,22 @@ "Genotypes", "Genotypes" ] + ], + "Scripps-2013": [ + [ + "Anterior Cingulate Cortex mRNA", + "Anterior Cingulate Cortex mRNA" + ] + ], + "UTHSC-Cannabinoid": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Genotypes", + "Genotypes" + ] ] }, "poplar": { @@ -5665,16 +7386,6 @@ ] }, "rat": { - "HRDP": [ - [ - "Phenotypes", - "Phenotypes" - ], - [ - "Genotypes", - "Genotypes" - ] - ], "HSNIH-Palmer": [ [ "Phenotypes", -- cgit v1.2.3 From 1b83ff353bf86709643c671ff78a69fd9ede72a8 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Mon, 27 Apr 2020 16:57:43 -0500 Subject: Added a script for a default runner --- etc/default_settings.py | 2 ++ scripts/run_debug.sh | 20 ++++++++++++++++++++ 2 files changed, 22 insertions(+) create mode 100755 scripts/run_debug.sh diff --git a/etc/default_settings.py b/etc/default_settings.py index 75f84dc4..053b906d 100644 --- a/etc/default_settings.py +++ b/etc/default_settings.py @@ -28,6 +28,8 @@ GN_VERSION = open("../etc/VERSION","r").read() SQL_URI = "mysql://gn2:mysql_password@localhost/db_webqtl_s" SQL_ALCHEMY_POOL_RECYCLE = 3600 GN_SERVER_URL = "http://localhost:8880/" # REST API server +GN2_BASE_URL = "http://genenetwork.org/" # to pick up REST API +GN2_BRANCH_URL = GN2_BASE_URL # ---- Flask configuration (see website) TRAP_BAD_REQUEST_ERRORS = True diff --git a/scripts/run_debug.sh b/scripts/run_debug.sh new file mode 100755 index 00000000..be7ecdb8 --- /dev/null +++ b/scripts/run_debug.sh @@ -0,0 +1,20 @@ +#! /bin/bash +# +# PLEASE DO NOT CHANGE THIS FILE - copy it elsewhere to run +# +# Run with GN2_PROFILE and SERVER_PORT overrides, e.g. +# +# env GN2_PROFILE=/usr/local/guix-profiles/gn-latest SERVER_PORT=5010 scripts/run_debug.sh + +[ -z $GN2_PROFILE ] && export GN2_PROFILE=/usr/local/guix-profiles/gn-latest +[ -z $SERVER_PORT ] && export SERVER_PORT=5010 + +echo Running on port $SERVER_PORT from $GN2_PROFILE + +cwd=`pwd` +echo Running source from $cwd + +mkdir -p ~/tmp + +env TMPDIR=~/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG GENENETWORK_FILES=/export/data/genenetwork/genotype_files/ SQL_URI=mysql://webqtlout:webqtlout@localhost/db_webqtl ./bin/genenetwork2 etc/default_settings.py -gunicorn-dev + -- cgit v1.2.3 From 0bca6569530d100291f176d04df8af9700705231 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Mon, 27 Apr 2020 17:12:54 -0500 Subject: settings: force SERVER_PORT to align with environment variable --- etc/default_settings.py | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/etc/default_settings.py b/etc/default_settings.py index 053b906d..176ee59c 100644 --- a/etc/default_settings.py +++ b/etc/default_settings.py @@ -40,7 +40,13 @@ SECURITY_RECOVERABLE = True SECURITY_EMAIL_SENDER = "no-reply@genenetwork.org" SECURITY_POST_LOGIN_VIEW = "/thank_you" -SERVER_PORT = 5003 # running on localhost +# ---- SERVER_PORT needs an override before firing up the server +SERVER_PORT = os.environ['SERVER_PORT'] +if isinstance(SERVER_PORT, str): + SERVER_PORT = int(SERVER_PORT) # don't do this for other settings! +else: + SERVER_PORT = 5003 + SECRET_HMAC_CODE = '\x08\xdf\xfa\x93N\x80\xd9\\H@\\\x9f`\x98d^\xb4a;\xc6OM\x946a\xbc\xfc\x80:*\xebc' GITHUB_CLIENT_ID = "UNKNOWN" -- cgit v1.2.3 From 9ec149a6a7498fc812ed4a44fa85bb746475a253 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Tue, 28 Apr 2020 08:32:00 -0500 Subject: Track requests and check for attribute so at least we get the right error: GeneNetwork penguin2:genenetwork2:2.11-rc2-penguin2-0bca65695 http://gn2-test3.genenetwork.org/ ( 1:31PM UTC Apr 28, 2020) MISCONF Redis is configured to save RDB snapshots, but is currently not able to persist on disk. Commands that may modify the data set are disabled. Please check Redis logs for details about the error. (error) File "/home/wrk/opt/genenetwork2/lib/python2.7/site-packages/redis/connection.py", line 717, in read_response --- wqflask/wqflask/templates/base.html | 2 ++ wqflask/wqflask/user_manager.py | 3 ++- wqflask/wqflask/user_session.py | 21 +++++++++++++-------- wqflask/wqflask/views.py | 1 + 4 files changed, 18 insertions(+), 9 deletions(-) diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html index 487cf3f2..abe14831 100644 --- a/wqflask/wqflask/templates/base.html +++ b/wqflask/wqflask/templates/base.html @@ -72,6 +72,7 @@
  • Interplanetary File System
    • + {% if g.user_session %}
  • Collections {{ g.user_session.num_collections }} @@ -93,6 +94,7 @@ Sign in {% endif %}
    • + {% endif %}