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_noeb_0217/notes.rtf | 23 ++ .../Uthsc_ilm_bxd_hipp_noeb_0217/specifics.rtf | 392 +++++++++++++++++++++ .../Uthsc_ilm_bxd_hipp_noeb_0217/summary.rtf | 39 ++ 3 files changed, 454 insertions(+) create mode 100644 general/datasets/Uthsc_ilm_bxd_hipp_noeb_0217/notes.rtf create mode 100644 general/datasets/Uthsc_ilm_bxd_hipp_noeb_0217/specifics.rtf create mode 100644 general/datasets/Uthsc_ilm_bxd_hipp_noeb_0217/summary.rtf (limited to 'general/datasets/Uthsc_ilm_bxd_hipp_noeb_0217') diff --git a/general/datasets/Uthsc_ilm_bxd_hipp_noeb_0217/notes.rtf b/general/datasets/Uthsc_ilm_bxd_hipp_noeb_0217/notes.rtf new file mode 100644 index 0000000..35247b6 --- /dev/null +++ b/general/datasets/Uthsc_ilm_bxd_hipp_noeb_0217/notes.rtf @@ -0,0 +1,23 @@ +

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

+ +
    +
  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_noeb_0217/specifics.rtf b/general/datasets/Uthsc_ilm_bxd_hipp_noeb_0217/specifics.rtf new file mode 100644 index 0000000..340fc0e --- /dev/null +++ b/general/datasets/Uthsc_ilm_bxd_hipp_noeb_0217/specifics.rtf @@ -0,0 +1,392 @@ +

NOE = No restraint stress and given an ethanol injection prior to sacrifice.

+ +
+ + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Index Array ID Condition Strain Sex Age
14060001078_DNOEBXD34F75
24060001088_ANOEBXD43F67
34207851040_CNOEBXD43F65
44207851040_DNOEBXD45F71
54207851041_CNOEBXD45M68
64068846016_DNOEBXD51F73
74207851035_DNOEBXD51M85
84060001003_CNOEBXD55F79
94068846016_CNOEBXD55M68
104060001071_ANOEBXD60F76
114068846016_ANOEBXD60M67
124060001003_DNOEBXD61M67
134207851041_ANOEBXD61F70
144060001075_FNOEBXD62M68
154207851041_BNOEBXD62F67
164207851035_ANOEBXD66F73
174256265071_CNOEBXD66M63
184207851035_BNOEBXD68M66
194256265026_ENOEBXD68F67
204060001010_FNOEBXD70M87
214207851045_BNOEBXD70F69
224256265057_ANOEBXD71F76
234256265087_CNOEBXD71M75
244256265042_BNOEBXD73F66
254060001010_ENOEBXD75F70
264256265042_CNOEBXD75M69
274060001083_ANOEBXD83M69
284256265071_DNOEBXD83F80
294256265045_CNOEBXD84F68
304207851058_ANOEBXD87F63
314256265080_CNOEBXD87M65
324207851058_BNOEBXD89M68
334256265024_ANOEBXD89F71
344256265024_BNOEBXD90F68
354256265052_ANOEBXD90M74
364256265023_ANOEBXD96M68
374256265023_FNOEBXD96F68
384256265044_ANOEBXD96M68
394068846017_BNOEBXD97M67
404068846017_ANOEBXD98F74
414207851052_FNOEBXD98M71
424068846021_FNOEBXD99M70
434060001088_ENOEBXD100F61
444060001088_DNOEBXD101M71
454060001030_DNOEDBA/2JF79
464256265069_FNOEDBA/2JF79
+
+
diff --git a/general/datasets/Uthsc_ilm_bxd_hipp_noeb_0217/summary.rtf b/general/datasets/Uthsc_ilm_bxd_hipp_noeb_0217/summary.rtf new file mode 100644 index 0000000..5aeb69c --- /dev/null +++ b/general/datasets/Uthsc_ilm_bxd_hipp_noeb_0217/summary.rtf @@ -0,0 +1,39 @@ +

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.

+ +

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.

+ +

Restraint Stress Protocol

+ +
    +
  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.
    4. +
  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).
    5. +
  5. Place each animal into zero-maze for 10 minutes.
    6. +
  6. Return animal to home cage.
    7. +
  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.
    8. +
+ +

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).

+ +

"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."

+ +

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.

+ +

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

+ +
    +
  1. NON: 669 (n=27 BXDs), 86.5 for B3galt6 (ILM50195)
    2. +
  2. NOS: 844 (n=28 BXDs), 100.2 for Telo2 (ILM4850047)
    3. +
  3. NOE: 1186 (n=35 BXDs), 101.9 for Mela-associated pseudogene (ILM4850047)
    4. +
  4. RSS: 725 (n=27 BXDs), 82.8 for Gpr116 (ILM105390524)
    5. +
  5. RSE: 915 (n=29 BXDs), 100.6 for Casp9 (ILM60577)
    6. +
+ +

Entered by Arthur Centeno, September 20, 2010.

+ +

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

+ +

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

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