RNA Extraction
+ +Total RNA was extracted using MIRNEASY MINI KIT (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. Approximately 30 mg of left ventricle tissue was added into a 2 ml tube containing 700ul QIAzol Lysis Reagent and one 5 mm stainless steel bead (Qiagen, Hilden, Germany). The tissue was homogenized for 2 minutes in a Tissue Lyser II (Qiagen, Hilden, Germany) with a speed frequency of 30 r followed by incubating for 5 minutes.140 µl chloroform was added into the homogenate, shaken vigorously for 15 seconds, and centrifuged for 15 minutes at 12,000 x g at 4 ℃. 280 µl upper aqueous was then transferred into a new collection tube containing 500 µl 100% ethanol. The mixture was loaded into a RNeasy miniâ€spin column (Qiagen, Valencia, CA, USA), once with Buffer RWT and twice with Buffer RPE purification. All RNA had been verified by Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). RNA with OD260/280 > 1.8 and RIN > 8.0 were used for library preparation
diff --git a/general/datasets/Nhlbi_bxd_young_adult_heart_cd_rna_seq/processing.rtf b/general/datasets/Nhlbi_bxd_young_adult_heart_cd_rna_seq/processing.rtf new file mode 100644 index 0000000..8e460ff --- /dev/null +++ b/general/datasets/Nhlbi_bxd_young_adult_heart_cd_rna_seq/processing.rtf @@ -0,0 +1,9 @@ +Generation of RNA-seq data
+ +1 µg of RNA was used for cDNA library construction at Novogene using an NEBNext® Ultra RNA Library Prep Kit for Illumina® (cat# E7420S, New England Biolabs, Ipswich, MA, USA) according to the manufacturer’s protocol. Briefly, mRNA was enriched using oligo(dT) beads followed by two rounds of purification and fragmented randomly by adding fragmentation buffer. The first strand cDNA was synthesized using random hexamers primer, after which a custom second-strand synthesis buffer (Illumina, San Diego, CA, USA), dNTPs, RNase H and DNA polymerase I were added to generate the second strand (ds cDNA). After a series of terminal repair, poly-adenylation, and sequencing adaptor ligation, the double-stranded cDNA library was completed following size selection and PCR enrichment. The resulting 250-350 bp insert libraries were quantified using a Qubit 2.0 fluorometer (Thermo Fisher Scientific, Waltham, MA, USA) and quantitative PCR. Size distribution was analyzed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Qualified libraries were sequenced on an Illumina Novaseq Platform (Illumina, San Diego, CA, USA) using a paired-end 150 run (2×150 bases). An average of 40 million raw reads were generated from each library.
+ ++ +
Read mapping and normalization
+ +Mus musculus (mouse) reference genome (GRCm38) and gene model annotation files were downloaded from the Ensembl genome browser (https://useast.ensembl.org/). Indices of the reference genome were built using STAR v2.5.0a and paired-end reads were aligned to the reference genome. STAR used the method of Maximal Mappable Prefix which can generate a precise mapping result for junction reads. FeatureCount v0.6.1 was used to count the number of read mapped to each gene. Transcripts Per Million (TPM) was calculated for each gene based on the length of the gene and reads mapped to that gene. In this normalization, the sum of all TPMs (genes-level) are equal to 1,000,000. The TPM was further rescaled to log2(TPM+1).
diff --git a/general/datasets/Nhlbi_bxd_young_adult_heart_cd_rna_seq/specifics.rtf b/general/datasets/Nhlbi_bxd_young_adult_heart_cd_rna_seq/specifics.rtf new file mode 100644 index 0000000..96fa0b5 --- /dev/null +++ b/general/datasets/Nhlbi_bxd_young_adult_heart_cd_rna_seq/specifics.rtf @@ -0,0 +1,2302 @@ +NHLBI BXD Young Adult Heart CD RNA-Seq (Nov20) TMP Log2
+ +About the cases used to generate this set of data:
+ +The study included 87 mice (~6 month) from B6, D2, and 41 advanced intercross BXD strains (about 2 mice per strain). All mice were fed on chow diet (CD). All procedures were approved by the UTHSC Institutional Animal Care and Use Committee.
+ ++ +
The table of samples that are finally used for this study.
+ +|
+ Index + |
+
+ Sample ID + |
+
+ Case id + |
+
+ Strain + |
+
+ Fuyi_Sex_Final + |
+
+ Age (Day) + |
+
+ Tissue + |
+
+ Diet + |
+
|
+ 1 + |
+
+ H100 + |
+
+ *091317.07 + |
+
+ BXD61 + |
+
+ M + |
+
+ 128 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 2 + |
+
+ H101 + |
+
+ *052417.59 + |
+
+ BXD177 + |
+
+ F + |
+
+ 125 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 3 + |
+
+ H102 + |
+
+ *052417.26 + |
+
+ BXD73a + |
+
+ F + |
+
+ 141 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 4 + |
+
+ H103 + |
+
+ *060717.02 + |
+
+ BXD9 + |
+
+ M + |
+
+ 149 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 5 + |
+
+ H109 + |
+
+ *052417.49 + |
+
+ BXD152 + |
+
+ F + |
+
+ 147 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 6 + |
+
+ H110 + |
+
+ *052417.35 + |
+
+ BXD86 + |
+
+ F + |
+
+ 127 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 7 + |
+
+ H112 + |
+
+ *052417.24 + |
+
+ BXD73 + |
+
+ F + |
+
+ 173 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 8 + |
+
+ H113 + |
+
+ *052417.25 + |
+
+ BXD73 + |
+
+ M + |
+
+ 173 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 9 + |
+
+ H116 + |
+
+ *121917.28 + |
+
+ BXD180 + |
+
+ F + |
+
+ 120 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 10 + |
+
+ H11 + |
+
+ *121917.20 + |
+
+ BXD111 + |
+
+ M + |
+
+ 122 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 11 + |
+
+ H120 + |
+
+ *111417.04 + |
+
+ BXD40 + |
+
+ M + |
+
+ 133 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 12 + |
+
+ H121 + |
+
+ *091317.02 + |
+
+ BXD48a + |
+
+ M + |
+
+ 125 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 13 + |
+
+ H122 + |
+
+ *092717.59 + |
+
+ BXD154 + |
+
+ F + |
+
+ 135 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 14 + |
+
+ H124 + |
+
+ *092717.60 + |
+
+ BXD154 + |
+
+ F + |
+
+ 135 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 15 + |
+
+ H126 + |
+
+ *092717.65 + |
+
+ BXD155 + |
+
+ F + |
+
+ 133 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 16 + |
+
+ H127 + |
+
+ *092717.67 + |
+
+ BXD169 + |
+
+ M + |
+
+ 133 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 17 + |
+
+ H129 + |
+
+ *092717.37 + |
+
+ BXD78 + |
+
+ F + |
+
+ 133 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 18 + |
+
+ H12 + |
+
+ *121917.21 + |
+
+ BXD111 + |
+
+ M + |
+
+ 122 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 19 + |
+
+ H130 + |
+
+ AGE050118.27 + |
+
+ DBA/2J + |
+
+ F + |
+
+ 167 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 20 + |
+
+ H131 + |
+
+ AGE050118.28 + |
+
+ DBA/2J + |
+
+ F + |
+
+ 167 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 21 + |
+
+ H132 + |
+
+ AGE050118.29 + |
+
+ DBA/2J + |
+
+ M + |
+
+ 167 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 22 + |
+
+ H138 + |
+
+ *112118.32 + |
+
+ C57BL/6J + |
+
+ F + |
+
+ 208 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 23 + |
+
+ H139 + |
+
+ *112118.33 + |
+
+ C57BL/6J + |
+
+ F + |
+
+ 208 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 24 + |
+
+ H140 + |
+
+ *112118.34 + |
+
+ C57BL/6J + |
+
+ F + |
+
+ 208 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 25 + |
+
+ H14 + |
+
+ *092017.36 + |
+
+ BXD113 + |
+
+ F + |
+
+ 132 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 26 + |
+
+ H15 + |
+
+ *092017.37 + |
+
+ BXD113 + |
+
+ M + |
+
+ 132 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 27 + |
+
+ H16 + |
+
+ *060717.15 + |
+
+ BXD123 + |
+
+ F + |
+
+ 182 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 28 + |
+
+ H17 + |
+
+ *060717.16 + |
+
+ BXD123 + |
+
+ M + |
+
+ 182 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 29 + |
+
+ H19 + |
+
+ *052417.44 + |
+
+ BXD128 (WAS b) + |
+
+ F + |
+
+ 161 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 30 + |
+
+ H20 + |
+
+ *052417.45 + |
+
+ BXD128 (WAS b) + |
+
+ F + |
+
+ 161 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 31 + |
+
+ H21 + |
+
+ *092017.38 + |
+
+ BXD144 + |
+
+ F + |
+
+ 133 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 32 + |
+
+ H23 + |
+
+ *092017.39 + |
+
+ BXD144 + |
+
+ M + |
+
+ 133 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 33 + |
+
+ H25 + |
+
+ *060717.03 + |
+
+ BXD15 + |
+
+ F + |
+
+ 143 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 34 + |
+
+ H26 + |
+
+ *060717.04 + |
+
+ BXD15 + |
+
+ F + |
+
+ 143 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 35 + |
+
+ H27 + |
+
+ *052417.47 + |
+
+ BXD151 + |
+
+ F + |
+
+ 127 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 36 + |
+
+ H28 + |
+
+ *092017.40 + |
+
+ BXD151 + |
+
+ M + |
+
+ 133 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 37 + |
+
+ H30 + |
+
+ *052417.51 + |
+
+ BXD152 + |
+
+ M + |
+
+ 147 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 38 + |
+
+ H31 + |
+
+ *052417.54 + |
+
+ BXD155 + |
+
+ M + |
+
+ 119 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 39 + |
+
+ H32 + |
+
+ *091317.01 + |
+
+ BXD16 + |
+
+ F + |
+
+ 128 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 40 + |
+
+ H33 + |
+
+ *111417.11 + |
+
+ BXD169 + |
+
+ F + |
+
+ 121 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 41 + |
+
+ H36 + |
+
+ *121917.16 + |
+
+ BXD171 + |
+
+ F + |
+
+ 124 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 42 + |
+
+ H38 + |
+
+ *092017.41 + |
+
+ BXD171 + |
+
+ M + |
+
+ 133 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 43 + |
+
+ H41 + |
+
+ *052417.60 + |
+
+ BXD177 + |
+
+ M + |
+
+ 125 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 44 + |
+
+ H43 + |
+
+ *052417.62 + |
+
+ BXD180 + |
+
+ M + |
+
+ 119 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 45 + |
+
+ H44 + |
+
+ *052417.32 + |
+
+ BXD83 + |
+
+ F + |
+
+ 155 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 46 + |
+
+ H46 + |
+
+ *052417.28 + |
+
+ BXD73a + |
+
+ M + |
+
+ 141 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 47 + |
+
+ H48 + |
+
+ *052417.40 + |
+
+ BXD89 + |
+
+ M + |
+
+ 173 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 48 + |
+
+ H49 + |
+
+ *060717.09 + |
+
+ BXD63 + |
+
+ F + |
+
+ 160 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 49 + |
+
+ H50 + |
+
+ *060717.06 + |
+
+ BXD24 + |
+
+ M + |
+
+ 138 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 50 + |
+
+ H51 + |
+
+ *060717.07 + |
+
+ BXD48 + |
+
+ F + |
+
+ 134 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 51 + |
+
+ H52 + |
+
+ *060717.08 + |
+
+ BXD48 + |
+
+ F + |
+
+ 134 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 52 + |
+
+ H53 + |
+
+ *060717.11 + |
+
+ BXD63 + |
+
+ M + |
+
+ 160 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 53 + |
+
+ H54 + |
+
+ *052417.22 + |
+
+ BXD62 + |
+
+ M + |
+
+ 165 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 54 + |
+
+ H55 + |
+
+ *052417.17 + |
+
+ BXD51 + |
+
+ F + |
+
+ 154 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 55 + |
+
+ H56 + |
+
+ *052417.15 + |
+
+ BXD50 + |
+
+ F + |
+
+ 167 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 56 + |
+
+ H57 + |
+
+ *052417.08 + |
+
+ BXD32 + |
+
+ M + |
+
+ 156 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 57 + |
+
+ H59 + |
+
+ *052417.21 + |
+
+ BXD62 + |
+
+ F + |
+
+ 165 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 58 + |
+
+ H60 + |
+
+ *052417.19 + |
+
+ BXD51 + |
+
+ M + |
+
+ 154 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 59 + |
+
+ H61 + |
+
+ *052417.16 + |
+
+ BXD50 + |
+
+ M + |
+
+ 167 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 60 + |
+
+ H62 + |
+
+ *052417.37 + |
+
+ BXD86 + |
+
+ M + |
+
+ 127 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 61 + |
+
+ H63 + |
+
+ *052417.29 + |
+
+ BXD73b + |
+
+ F + |
+
+ 145 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 62 + |
+
+ H64 + |
+
+ *052417.31 + |
+
+ BXD73b + |
+
+ M + |
+
+ 145 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 63 + |
+
+ H65 + |
+
+ *121917.01 + |
+
+ BXD43 + |
+
+ F + |
+
+ 126 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 64 + |
+
+ H66 + |
+
+ *121917.13 + |
+
+ BXD45 + |
+
+ M + |
+
+ 126 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 65 + |
+
+ H67 + |
+
+ *121917.12 + |
+
+ BXD45 + |
+
+ F + |
+
+ 126 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 66 + |
+
+ H68 + |
+
+ *121917.02 + |
+
+ BXD43 + |
+
+ F + |
+
+ 126 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 67 + |
+
+ H69 + |
+
+ *071917.35 + |
+
+ BXD68 + |
+
+ M + |
+
+ 134 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 68 + |
+
+ H71 + |
+
+ *092017.32 + |
+
+ BXD83 + |
+
+ M + |
+
+ 136 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 69 + |
+
+ H72 + |
+
+ *092017.30 + |
+
+ BXD78 + |
+
+ M + |
+
+ 132 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 70 + |
+
+ H74 + |
+
+ *092017.29 + |
+
+ BXD75 + |
+
+ M + |
+
+ 133 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 71 + |
+
+ H76 + |
+
+ *092017.26 + |
+
+ BXD75 + |
+
+ F + |
+
+ 133 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 72 + |
+
+ H78 + |
+
+ *092017.05 + |
+
+ BXD40 + |
+
+ F + |
+
+ 128 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 73 + |
+
+ H79 + |
+
+ *092017.02 + |
+
+ BXD24 + |
+
+ F + |
+
+ 131 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 74 + |
+
+ H80 + |
+
+ *092017.01 + |
+
+ BXD9 + |
+
+ F + |
+
+ 129 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 75 + |
+
+ H81 + |
+
+ *092017.12 + |
+
+ BXD65 + |
+
+ F + |
+
+ 132 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 76 + |
+
+ H83 + |
+
+ *092017.33 + |
+
+ BXD89 + |
+
+ F + |
+
+ 136 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 77 + |
+
+ H84 + |
+
+ *092017.23 + |
+
+ BXD70 + |
+
+ F + |
+
+ 130 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 78 + |
+
+ H85 + |
+
+ *092017.22 + |
+
+ BXD70 + |
+
+ F + |
+
+ 127 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 79 + |
+
+ H86 + |
+
+ *092017.07 + |
+
+ BXD44 + |
+
+ F + |
+
+ 128 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 80 + |
+
+ H89 + |
+
+ *092017.14 + |
+
+ BXD65 + |
+
+ M + |
+
+ 132 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 81 + |
+
+ H90 + |
+
+ *092017.03 + |
+
+ BXD32 + |
+
+ F + |
+
+ 131 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 82 + |
+
+ H91 + |
+
+ *092017.20 + |
+
+ BXD65b + |
+
+ M + |
+
+ 130 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 83 + |
+
+ H92 + |
+
+ *092017.09 + |
+
+ BXD44 + |
+
+ F + |
+
+ 128 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 84 + |
+
+ H94 + |
+
+ *092017.18 + |
+
+ BXD65b + |
+
+ F + |
+
+ 130 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 85 + |
+
+ H96 + |
+
+ *091317.06 + |
+
+ BXD61 + |
+
+ M + |
+
+ 128 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 86 + |
+
+ H97 + |
+
+ *091317.12 + |
+
+ BXD68 + |
+
+ F + |
+
+ 132 + |
+
+ Heart + |
+
+ Chow diet + |
+
|
+ 87 + |
+
+ H99 + |
+
+ *091317.04 + |
+
+ BXD48a + |
+
+ M + |
+
+ 125 + |
+
+ Heart + |
+
+ Chow diet + |
+
Tissue Harvest
+ +The animals were sacrificed under saturated isoflurane. Whole heart from the animals were dissected and stored at −80°C until RNA extraction.
-- cgit v1.2.3