From b2feda451ccfbeaed02dce9088d6dd228cf15861 Mon Sep 17 00:00:00 2001 From: Bonface Date: Tue, 13 Feb 2024 23:52:26 -0600 Subject: Update dataset RTF Files. --- .../UTHSC_ILM_BXD_hipp_RSSb_0217/notes.rtf | 23 -- .../UTHSC_ILM_BXD_hipp_RSSb_0217/specifics.rtf | 400 --------------------- .../UTHSC_ILM_BXD_hipp_RSSb_0217/summary.rtf | 39 -- 3 files changed, 462 deletions(-) delete mode 100644 general/datasets/UTHSC_ILM_BXD_hipp_RSSb_0217/notes.rtf delete mode 100644 general/datasets/UTHSC_ILM_BXD_hipp_RSSb_0217/specifics.rtf delete mode 100644 general/datasets/UTHSC_ILM_BXD_hipp_RSSb_0217/summary.rtf (limited to 'general/datasets/UTHSC_ILM_BXD_hipp_RSSb_0217') diff --git a/general/datasets/UTHSC_ILM_BXD_hipp_RSSb_0217/notes.rtf b/general/datasets/UTHSC_ILM_BXD_hipp_RSSb_0217/notes.rtf deleted file mode 100644 index 35247b6..0000000 --- a/general/datasets/UTHSC_ILM_BXD_hipp_RSSb_0217/notes.rtf +++ /dev/null @@ -1,23 +0,0 @@ -

Hippocampus 5 Conditions
-Illumina Rank Invariant Normalized; Log2 Transformed and Z-Scored
-Batch and Outlier Analysis on Partek Genomic Suite 6.6
-ANOVA Done with batch (BATCH 1 AND 2); Batch effect removed
-K MOZHUI (KMOZHUI@UTHSC.EDU) 12-Nov-12
-Outliers removed are: 4060001003_A, 4060001010_D, 4060001012_A, 4060001012_C, 4060001012_E, AND 4060001078_A
-Number of samples = 284
-Number of probes = 46643

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  1. UTHSC Hippocampus Illumina v6.1 5Trt (Nov12) RankInv LRS=(46 999)-> 1331
    - ProbeSetID:ILM3440048 Gene:Cdkl2 Max LRS=192
    2. -
  2. UTHSC Hippocampus Illumina v6.1 NON (Nov12) RankInv LRS=(46 999)-> 219
    - ProbeSetID:ILM6350725 Gene:C14orf119 Max LRS=97.8
    3. -
  3. UTHSC Hippocampus Illumina v6.1 NOS (Nov12) RankInv LRS=(46 999)-> 404
    - ProbeSetID:ILM3440048 Gene:Cdkl2 Max LRS=106.6
    4. -
  4. UTHSC Hippocampus Illumina v6.1 NOE (Nov12) RankInv LRS=(46 999)-> 509
    - ProbeSetID:ILM5270066 Gene:MGC67181 Max LRS=151
    5. -
  5. UTHSC Hippocampus Illumina v6.1 RSS (Nov12) RankInv LRS=(46 999)-> 415
    - ProbeSetID:ILM5720687 Gene:Abhd16a Max LRS=121.7
    6. -
  6. UTHSC Hippocampus Illumina v6.1 RSE (Nov12) RankInv LRS=(46 999)-> 421
    - ProbeSetID:ILM6350725 Gene:C14orf119 Max LRS=144.1
    7. -
diff --git a/general/datasets/UTHSC_ILM_BXD_hipp_RSSb_0217/specifics.rtf b/general/datasets/UTHSC_ILM_BXD_hipp_RSSb_0217/specifics.rtf deleted file mode 100644 index 6036ccb..0000000 --- a/general/datasets/UTHSC_ILM_BXD_hipp_RSSb_0217/specifics.rtf +++ /dev/null @@ -1,400 +0,0 @@ -

RSS = short restraint stress (1 episode) followed by a saline injection.

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Index Array ID Condition Strain Sex Age
14207851045_DRSSBXD34M71
24060001083_BRSSBXD43M72
34068846017_CRSSBXD43F73
44060001083_FRSSBXD45F67
54256265070_DRSSBXD45M79
64060001096_FRSSBXD51M75
74256265045_ERSSBXD51F88
84256265043_BRSSBXD55F67
94256265024_DRSSBXD60M76
104256265045_FRSSBXD60F72
114207851058_DRSSBXD61F70
124256265083_BRSSBXD61M82
134068846017_ERSSBXD62F61
144256265080_FRSSBXD62M67
154207851052_ARSSBXD66M74
164256265044_BRSSBXD66F69
174060001003_ERSSBXD68F77
184060001075_CRSSBXD68M64
194068846021_ERSSBXD70M68
204207851038_CRSSBXD70F69
214060001003_FRSSBXD71M78
224060001011_ERSSBXD71F76
234207851014_ARSSBXD73F68
244207851014_DRSSBXD73M67
254051964017_ARSSBXD75F73
264256265058_BRSSBXD75F69
274256265058_CRSSBXD83F75
284256265074_FRSSBXD83M69
294256265062_BRSSBXD84F73
304256265086_BRSSBXD84M69
314207851051_FRSSBXD87M69
324256265083_ARSSBXD89F59
334256265073_ARSSBXD90F68
344256265087_FRSSBXD90M68
354207851051_BRSSBXD96M69
364256265085_CRSSBXD96F76
374060001079_FRSSBXD97F65
384256265080_ARSSBXD97M70
394060001011_FRSSBXD98M72
404256265086_ARSSBXD98F72
414207851014_CRSSBXD99M73
424256265086_CRSSBXD99F86
434060001068_FRSSBXD100M79
444207851051_DRSSBXD100F68
454207851045_CRSSBXD101F66
464060001012_FRSSDBA/2JF70
474060001031_DRSSDBA/2JF70
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-
diff --git a/general/datasets/UTHSC_ILM_BXD_hipp_RSSb_0217/summary.rtf b/general/datasets/UTHSC_ILM_BXD_hipp_RSSb_0217/summary.rtf deleted file mode 100644 index 5aeb69c..0000000 --- a/general/datasets/UTHSC_ILM_BXD_hipp_RSSb_0217/summary.rtf +++ /dev/null @@ -1,39 +0,0 @@ -

This is untreated control "Base" group gene expression data for the hippocampus of BXD strains of mice (n = 27 strains and n = 35 animals). These data NON data are useful as baseline for comparison with NOS, NOE, RSS, and RSE data sets. NON = NON = No stress and no saline control injection; NOS = No restraint stress and given only saline injections prior to sacrifice; NOE = No restraint stress and given an ethanol injection prior to sacrifice; RSS = short restraint stress (1 episode) followed by a saline injection; and finally, RSE = Restraint stress followed by an ethanol injection.

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For more details on the precise experimental paradigm, please see Ziebarth et al 2010 or the original paper that used this paradigm by Kerns RT, Ravindranathan A, Hassan S, Cage MP, York T, Williams RW, Miles MF (2005) Ethanol-responsive brain region expression networks: implications for behavioral responses to acute ethanol in DBA/2J versus C57BL/6J mice. Journal of Neuroscience 25: 2255-2266.

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Restraint Stress Protocol

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  1. Weigh animals all animals to be tested and record body weight.
    2. -
  2. Bring animals into testing area at least one hour prior to testing. 9 a.m. The following steps will be done for three animals (in parallel) because we have three zero-mazes.
    3. -
  3. Place animals in immobilization tubes for 15 minutes.
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  4. Inject animals IP with saline OR ethanol* and return to home cages for 5 minutes. (Remember to counterbalance groups. All animals in one cage should not be assigned to same group).
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  5. Place each animal into zero-maze for 10 minutes.
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  6. Return animal to home cage.
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  7. Exactly 4 hours after injection, kill animals and remove brains to RNAlater solution. Animals should be killed by rapid decapitation with scissors so that trunk blood can be collected at the same time for corticosteroid analysis.
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Ethanol and saline injections
-Ethanol will be mixed with saline : 12.5% v/v. 100 ml of solution = 87.5 ml of saline and 12.5 ml of ethanol. Animals receive an injection of 1.8 g/kg. Multiply animals’ body weight by 0.018 to get injection volume (i.e. 25 g mouse X .018 mL/g = 0.45mL injection volume).

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"Adult mice were housed three to five to a cage with ad libitum access to standard rodent chow (Harlan Teklad, Madison, WI) and water in a 12 h dark/light cycle. All injections were intraperitoneal. Mice were given a saline injection once daily for 5 d to habituate them to the injection process. On day 6, mice received either an injection of saline or 20% ethanol in saline."

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Data Quality: All five data have been error checked. Strain and sex assignments were verified and are correct. This was determined by analysis of approximately 20 "test Mendelian" probes such as that for Thumpd1 (ILM751048). These probes have very high LRS values and the expected strain distribution pattern given their chromosomal location. Expression of genes on X and Y chromosomes (such as Xist) were used to confirm sex.

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Quality Control Data
-Total cis eQTLs with LRS > 23 within 5 Mb, maximum cis eQTL LRS value and probe

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  1. NON: 669 (n=27 BXDs), 86.5 for B3galt6 (ILM50195)
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  2. NOS: 844 (n=28 BXDs), 100.2 for Telo2 (ILM4850047)
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  3. NOE: 1186 (n=35 BXDs), 101.9 for Mela-associated pseudogene (ILM4850047)
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  4. RSS: 725 (n=27 BXDs), 82.8 for Gpr116 (ILM105390524)
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  5. RSE: 915 (n=29 BXDs), 100.6 for Casp9 (ILM60577)
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Entered by Arthur Centeno, September 20, 2010.

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Array data sets all generated by Dr. Lu Lu (2008 - 2009) at the University of Tennessee Health Science Center, Memphis.

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Corresponding anxiety and ethanol response phenotypes generated by Dr. Melloni Cook and colleagues at the University of Memphis.

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