Data Set Group2: INIA-UTHSC Midbrain CIE Affy MTA 1.0 RMA

Data Set: INIA-UTHSC Midbrain CIE Affy MTA 1.0 Exon Level (Apr17) RMA GN Accession: GN834 GEO Series: No Geo series yet Title: Organism: Mouse (Mus musculus, mm10) Group: CIE-RMA Tissue: Midbrain mRNA Dataset Status: Private Platforms: Affymetrix MTA Mouse Transcriptome Assay 1.0 Normalization: RMA

Contact Information Megan Mulligan University of Tennessee Health Science Center 855 Monroe Ave Suite 515 Memphis, Tennessee 38163 United States Tel. 5126802386 mmulliga@uthsc.edu Website Download datasets and supplementary data files

Specifics of this Data Set:

Exon Level

Summary:

Overview: 1. Treated and whole brains dissected at Medical University of South Carolina (Marcelo F. Lopez laboratory) 2. Frozen brains sub-dissected at UTHSC (Megan K. Mulligan laboratory) 3. RNA extraction (Qiagen RNeasy kit) at UTHSC (Mulligan and Williams laboratories) 4. Hybridized to Affymetrix Clariom D (aka Affymetrix MTA 1.0 ST) array at UTHSC MRC (Lorne Rose, UTHSC Molecular Resource Center) 5. Initial QC and normalization (COMBAT) at UTHSC (Megan K. Mulligan laboratory) 6. Transcriptome entry and phenotype entry (Arthur Centeno, Megan K. Mulligan, and Robert W. Williams)   Chronic ethanol exposure: Mice were allowed to self-administer alcohol (15% v/v vs. water) for 2 h a day (5 days a week) 6 weeks prior to treatment in order to establish baseline consumption. Access to 15% alcohol versus water started 30 min prior to the start of the dark cycle. Following establishment of baseline drinking, male mice representative of each strain were separated into groups to be exposed to either weekly cycles of CIE exposure (CIE group) or air control (AIR group) exposure.    Mice assigned to the CIE treatment group were exposed to alcohol vapor for 16 h a day followed by 8 h of withdrawal for 4 days per week. Following the fourth vapor exposure, mice were given a 72-h abstinence/withdrawal period before resuming ethanol intake in the home cage for 5 days. Mice in the AIR control treatment group were similarly treated but exposed only to air in the inhalation chambers. This pattern of CIE or air control exposure followed by 5 days of ethanol self-administration was repeated for four cycles. A fifth cycle of CIE (or air) exposure followed the fourth ethanol intake evaluation period, and brain tissue was collected at multiple time points (8h, 3d, 7d, 14d) after the last cycle ended. Pyrazole (1 mmol/kg) was used to stabilize blood ethanol levels (BEC) and was administered to both CIE and AIR groups. A subset of mice received no pyrazole.    Analysis: 1. Normalization on Affymetrix Expression Console (SST-RMA Gene Level). 2. Batch effect detected (RNA concentration dependent) and corrected in ComBat

About the cases used to generate this set of data:

MicroarrayID Mouse.ID Strain Pyrazole TimePoint Treatment PCA Batch DissectionBatch ExtractionBatch Concentration RIN MB1 12 C57BL/6J PZ 8h CIE B A 1 224.611   9.0 MB2 50 DBA/2J NO 3d AIR B A 1 195.150    9.2 MB3 2 C57BL/6J PZ 14d AIR B A 1 299.415   9.5 MB4 60 DBA/2J PZ 7d AIR B A 1 300.033   7.6 MB5 4 C57BL/6J PZ 14d CIE A A 1 249.226   7.2 MB6 69 DBA/2J PZ 7d AIR A A 1 161.526   7.3 MB7 8 C57BL/6J PZ 3d CIE B A 1 326.862   9.5 MB8 41 DBA/2J PZ 8h AIR B A 1 352.559   7.9 MB9 75 DBA/2J PZ 14d AIR B B 1 354.218   8.8 MB10 23 C57BL/6J PZ 3d AIR B B 1 280.396   9.6 MB11 49 DBA/2J PZ 3d AIR A B 1 180.312   7.2 MB12 58 DBA/2J PZ 3d CIE B B 1 225.072   NA MB13 21 C57BL/6J PZ 14d CIE B C 1 299.623   7.4 MB14 63 DBA/2J PZ 3d CIE B C 1 70.977   7.5 MB15 46 DBA/2J PZ 8h AIR B C 1 284.115   7.9 MB16 45 DBA/2J PZ 8h AIR B C 1 338.791   7.7 MB17 28 C57BL/6J NO 3d AIR B C 1 449.851   7.8 MB18 78 DBA/2J PZ 14d AIR B C 1 320.081   7.9 MB19 77 DBA/2J PZ 14d CIE B C 1 234.795   7.8 MB20 71 DBA/2J PZ 7d CIE B C 1 468.728   7.8 MB21 68 DBA/2J PZ 7d AIR B C 1 296.386   7.9 MB22 29 C57BL/6J PZ 8h CIE B C 1 398.481   8.0 MB23 67 DBA/2J PZ 7d CIE B A 2 275.813   7.8 MB24 1 C57BL/6J PZ 8h AIR A A 2 132.589   6.8 MB25 14 C57BL/6J NO 3d CIE A A 2 189.666   7.9 MB26 42 DBA/2J PZ 8h CIE B A 2 310.878   9.4 MB27 55 DBA/2J PZ 3d CIE B A 2 211.576   9.0 MB28 73 DBA/2J PZ 7d CIE B A 2 287.696   7.6 MB29 48 DBA/2J PZ 3d AIR B A 2 317.532   7.8 MB30 61 DBA/2J PZ 7d AIR B B 2 294.808   7.8 MB31 20 C57BL/6J PZ 8h CIE B B 2 209.301   9.0 MB32 76 DBA/2J PZ 14d CIE A B 2 120.953   8.2 MB33 5 C57BL/6J PZ 14d AIR B B 2 271.808   8.8 MB34 37 C57BL/6J PZ 7d CIE B B 2 289.261   8.0 MB35 19 C57BL/6J PZ 3d CIE B C 2 306.294   9.1 MB36 56 DBA/2J PZ 3d AIR B C 2 265.964   7.8 MB37 65 DBA/2J NO 3d CIE B C 2 259.741   9.2 MB38 80 DBA/2J PZ 14d AIR B C 2 371.000   8.0 MB39 31 C57BL/6J PZ 14d CIE B C 2 349.451   7.7 MB40 39 C57BL/6J PZ 7d AIR C C 2 403.083   8.9 MB41 62 DBA/2J PZ 3d CIE C C 2 505.547   8.9 MB42 52 DBA/2J PZ 8h CIE C C 2 441.549   8.8 MB43 51 DBA/2J PZ 3d AIR C C 2 519.427   8.8 MB44 35 C57BL/6J NO 3d AIR C A 3 772.361   8.8 MB45 72 DBA/2J PZ 14d AIR C A 3 598.185   8.9 MB46 32 C57BL/6J PZ 7d CIE C A 3 824.974   8.7 MB47 74 DBA/2J PZ 14d CIE C A 3 495.046   9.4 MB48 54 DBA/2J PZ 8h CIE C A 3 667.036   9.4 MB49 24 C57BL/6J PZ 7d AIR C A 3 760.367   9.2 MB50 9 C57BL/6J PZ 3d AIR C A 3 701.152   9.2 MB51 66 DBA/2J NO 3d CIE C B 3 579.22   8.3 MB52 44 DBA/2J PZ 8h CIE C B 3 636.091   9.4 MB53 34 C57BL/6J PZ 7d AIR C B 3 739.127   9.5 MB54 7 C57BL/6J PZ 8h AIR C B 3 667.933   9.2 MB55 36 C57BL/6J NO 3d CIE C C 3 605.937   9.2 MB56 43 DBA/2J PZ 8h AIR C C 3 639.161   9.5 MB57 70 DBA/2J PZ 7d CIE C C 3 630.735   9.4 MB58 59 DBA/2J NO 3d AIR C C 3 548.647   9.5 MB59 15 C57BL/6J PZ 14d AIR C C 3 689.793   9.4 MB60 27 C57BL/6J PZ 8h AIR C C 3 580.462   9.4 MB61 30 C57BL/6J PZ 3d AIR C C 3 577.826   8.2 MB62 57 DBA/2J PZ 3d AIR C C 3 581.164   9.0 MB63 38 C57BL/6J PZ 3d CIE C C 3 748.421   8.6 MB64 47 DBA/2J PZ 8h AIR C C 3 747.345   8.5

About the tissue used to generate this set of data:

About the array platform:

About data values and data processing:

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Experiment Type:

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Citation:

Data source acknowledgment:

Study Id:

264

• The UT Center for Integrative and Translational Genomics
• NIGMS Systems Genetics and Precision Medicine project (R01 GM123489, 2017-2021)
• NIDA NIDA Core Center of Excellence in Transcriptomics, Systems Genetics, and the Addictome (P30 DA044223, 2017-2022)
• NIA Translational Systems Genetics of Mitochondria, Metabolism, and Aging (R01AG043930, 2013-2018)
• NIAAA Integrative Neuroscience Initiative on Alcoholism (U01 AA016662, U01 AA013499, U24 AA013513, U01 AA014425, 2006-2017)
• NIDA, NIMH, and NIAAA (P20-DA 21131, 2001-2012)
• NCI MMHCC (U01CA105417), NCRR, BIRN, (U24 RR021760)