Data Set Group2: Hippocampus Mouse Transcriptome Assay 1.0 GeneLevel Main (Nov15) RMA

Data Set: Hippocampus Mouse Transcriptome Assay 1.0 GeneLevel Main (Nov15) RMA ** GN Accession: GN771 GEO Series: No Geo series yet Title: Unpublished Organism: Mouse (Mus musculus, mm10) Group: CMS Tissue: Hippocampus mRNA Dataset Status: Private Platforms: Affymetrix MTA Mouse Transcriptome Assay 1.0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 GN771_CMS_1Batch_All_Treat_NoOutliers_GeneLevel_RMA-Sketch_ZScore.txt.zip (N/A)

Specifics of this Data Set:

None

Summary:

This data set was generated to study the effects of strain and stress on hippocampal gene expression in female mice. The data set includes three inbred strains of mice and four treatment groups.

About the cases used to generate this set of data:

The original data set included four individuals of each strain under baseline (B) conditions and eight individuals from each strain for each of the treatment groups, chronic mild stress (C), acute restraint (R), and chronic mild stress followed by acute retraint (CR). However, some samples have been removed due to technical problems with tissue collection or microarray performance. MTA_ID MTA prefix GN_ID FM_ID Mouse_ID CaseId Strain Strain_Code Treatment code NanoDrop, ng/ul NanoDrop, 260/280 NanoDrop, 260/230 Agilent, ng/µl RIN Notes 1 BCJ 1.CMS_ D-B-215-1 CMS_000215 215 020615.01 DBA/2J D B 163.61 1.9 2.31 130 8.6   2 BCJ 2.CMS_ D-C-86-1 CMS_000086 86 012115.23 DBA/2J D C 98.51 1.79 2.4 329 8.8   3 BCJ 3.CMS_ D-CR-94-1 CMS_000094 94 012115.16 DBA/2J D CR 162.78 1.87 2.38 166 9.2   4 BCJ 4.CMS_ D-R-133-1 CMS_000133 133 012115.14 DBA/2J D R 88.95 1.82 2.45 90 8.2   5 BCJ 5.CMS_ B-B-208-1 CMS_000208 208 012215.04 C57BL/6J B B 129.24 1.86 2.41 223 8.1   6 BCJ 6.CMS_ B-C-101-1 CMS_000101 101 012115.25 C57BL/6J B C 72.29 1.86 2.26 135 9.2   7 BCJ 7.CMS_ B-CR-109-1 CMS_000109 109 012115.21 C57BL/6J B CR 158.56 1.7 2.46 305 8.8 Microarray outlier; sample removed. 8 BCJ 8.CMS_ B-R-143-1 CMS_000143 143 012215.08 C57BL/6J B R 161.57 1.86 2.38 217 9.3   9 BCJ 9.CMS_ N-B-210-1 CMS_000210 210 012115.04 C57BL/6NJ N B 132.39 1.89 2.3 192 8.5   10 BCJ 10.CMS_ N-C-117-1 CMS_000117 117 012115.30 C57BL/6NJ N C 151.43 1.91 2.38 187 8.8   11 BCJ 11.CMS_ N-CR-126-1 CMS_000126 126 012115.33 C57BL/6NJ N CR 137.87 1.88 2.29 76 9   12 BCJ 12.CMS_ N-R-152-1 CMS_000152 152 012215.29 C57BL/6NJ N R 197.95 1.88 2.35 150 9.1   13 BCJ 13.CMS_ D-B-216-1 CMS_000216 216 020615.02 DBA/2J D B 98.64 1.91 2.03 60 8.6   15 BCJ 15.CMS_ D-CR-93-1 CMS_000093 93 012115.11 DBA/2J D CR 71.36 1.83 2.25 109 8.5   16 BCJ 16.CMS_ D-R-134-1 CMS_000134 134 012115.17 DBA/2J D R 73.49 1.85 2.43 149 8.2   17 BCJ 17.CMS_ B-B-205-1 CMS_000205 205 012015.02 C57BL/6J B B 174.78 2.02 2.21 266 8.9   18 BCJ 18.CMS_ B-C-104-1 CMS_000104 104 012215.30 C57BL/6J B C 84.7 2.64 2.01 168 9.2   19 BCJ 19.CMS_ B-CR-110-1 CMS_000110 110 012115.26 C57BL/6J B CR 136.7 1.96 2.16 178 9.5   20 BCJ 20.CMS_ B-R-141-1 CMS_000141 141 012115.22 C57BL/6J B R 86.04 20.2 2.53 208 8.9   21 BCJ 21.CMS_ N-B-209-1 CMS_000209 209 012015.04 C57BL/6NJ N B 98.3 1.99 2.35 169 8.8   22 BCJ 22.CMS_ N-C-119-1 CMS_000119 119 012215.18 C57BL/6NJ N C 94.63 1.96 2.36 179 8.5   24 BCJ 24.CMS_ N-R-150-1 CMS_000150 150 012115.29 C57BL/6NJ N R 407.34 1.98 2.24 425 7.5 Microarray outlier; sample removed. 25 BCJ 25.CMS_ D-B-217-1 CMS_000217 217 020615.03 DBA/2J D B 84.61 1.82 2.18 177 7.9   26 BCJ 26.CMS_ D-C-85-1 CMS_000085 85 012115.20 DBA/2J D C 172.86 1.98 2.27 288 8.9   27 BCJ 27.CMS_ D-CR-95-1 CMS_000095 95 012215.16 DBA/2J D CR 109.8 1.98 2.47 157 8.9   28 BCJ 28.CMS_ D-R-132-1 CMS_000132 132 012015.29 DBA/2J D R 140.82 1.91 2.47 318 9   29 BCJ 29.CMS_ B-B-207-1 CMS_000207 207 012215.02 C57BL/6J B B 96.25 1.89 2.67 176 8.5   30 BCJ 30.CMS_ B-C-102-1 CMS_000102 102 012115.28 C57BL/6J B C 129.69 1.89 2.32 105 8.7   31 BCJ 31.CMS_ B-CR-111-1 CMS_000111 111 012215.26 C57BL/6J B CR 165.67 1.84 2.31 176 9.5   32 BCJ 32.CMS_ B-R-142-1 CMS_000142 142 012115.24 C57BL/6J B R 116.93 1.84 2.22 96 9.4   33 BCJ 33.CMS_ N-B-211-1 CMS_000211 211 012315.02 C57BL/6NJ N B 106 2.09 2.29 156 7.4   34 BCJ 34.CMS_ N-C-118-1 CMS_000118 118 012115.32 C57BL/6NJ N C 219.2 1.91 2.34 197 9.2   35 BCJ 35.CMS_ N-CR-127-1 CMS_000127 127 012215.33 C57BL/6NJ N CR 89 2 2.56 157 9.4   36 BCJ 36.CMS_ N-R-149-1 CMS_000149 149 012115.27 C57BL/6NJ N R 72.91 1.84 2.14 107 8.6   37 BCJ 37.CMS_ D-B-218-1 CMS_000218 218 020615.04 DBA/2J D B 154.34 1.99 1.99 119 9.3   38 BCJ 38.CMS_ D-C-87-1 CMS_000087 87 012215.13 DBA/2J D C 105.3 1.98 2.21 109 7.4   39 BCJ 39.CMS_ D-CR-97-1 CMS_000097 97 012315.05 DBA/2J D CR 55.85 1.89 2.41 85 8.3   40 BCJ 40.CMS_ D-R-137-1 CMS_000137 137 012315.06 DBA/2J D R 128.97 2.01 2.24 159 8.1 Microarray outlier; sample removed. 41 BCJ 41.CMS_ B-B-206-1 CMS_000206 206 012115.02 C57BL/6J B B 159.89 2.03 2.1 273 7.8   42 BCJ 42.CMS_ B-C-103-1 CMS_000103 103 012215.15 C57BL/6J B C 111.79 1.87 2.45 160 8.9   43 BCJ 43.CMS_ B-CR-112-1 CMS_000112 112 012215.31 C57BL/6J B CR 172.14 1.86 2.22 180 9.4   44 BCJ 44.CMS_ B-R-145-1 CMS_000145 145 012315.12 C57BL/6J B R 103.74 2.06 2.17 99 8.9   45 BCJ 45.CMS_ N-B-212-1 CMS_000212 212 012315.04 C57BL/6NJ N B 189.5 1.9 2.4 248 8.5   47 BCJ 47.CMS_ N-CR-128-1 CMS_000128 128 012215.34 C57BL/6NJ N CR 90.65 2.07 2.25 189 9.3   48 BCJ 48.CMS_ N-R-154-1 CMS_000154 154 012315.29 C57BL/6NJ N R 114.73 1.94 2.34 167 8.8   49 BCJ 49.CMS_ D-C-88-1 CMS_000088 88 012215.28 DBA/2J D C 96 1.76 2.55 158 8.5   50 BCJ 50.CMS_ D-CR-96-1 CMS_000096 96 012215.21 DBA/2J D CR 133.66 1.78 2.36 203 8.3   51 BCJ 51.CMS_ D-R-138-1 CMS_000138 138 012315.22 DBA/2J D R 127.13 1.76 2.24 81 9.3   52 BCJ 52.CMS_ B-C-105-1 CMS_000105 105 012315.13 C57BL/6J B C 203.24 1.92 2.35 310 7   53 BCJ 53.CMS_ B-CR-113-1 CMS_000113 113 012315.09 C57BL/6J B CR 168.67 1.82 2.41 240 9.1   55 BCJ 55.CMS_ N-C-120-1 CMS_000120 120 012215.32 C57BL/6NJ N C 73.67 1.93 2.31 371 8.4   56 BCJ 56.CMS_ N-CR-125-1 CMS_000125 125 012115.31 C57BL/6NJ N CR 121.93 1.92 2.26 73 8.3   59 BCJ 59.CMS_ N-C-122-1 CMS_000122 122 012315.30 C57BL/6NJ N C 131.74 1.85 2.42 186 9.4   60 BCJ 60.CMS_ D-C-89-1 CMS_000089 89 012315.10 DBA/2J D C 78 1.77 2.32 74 8.9   62 BCJ 62.CMS_ N-CR-130-1 CMS_000130 130 012315.34 C57BL/6NJ N CR 100.74 1.71 2.36 113 8.8   65 BCJ 65.CMS_ B-R-144-1 CMS_000144 144 012215.27 C57BL/6J B R 80.1 1.81 2.3 95 8.9   66 BCJ 66.CMS_ N-R-151-1 CMS_000151 151 012215.12 C57BL/6NJ N R 80.22 1.77 2.2 116 8.6

About the tissue used to generate this set of data:

This data set includes expression data from mouse hippocampus.

About the array platform:

About data values and data processing:

Outlier Detection. Samples 7 (J-CR-21), 24 (N-R-29), and 40 (D-R-6) were detected as outliers and have abnormal expression profiles (i.e. they do not cluster with other samples and have abnormal median and quartile ranges after normalization. These samples have been removed from the analysis. RMA Algorithm. The Robust Multichip Analysis (RMA) algorithm fits a robust linear model at the probe level to minimize the effect of probe-specific affinity differences. This approach: n Increases sensitivity to small changes between experiment and control samples. n Minimizes variance across the dynamic range, but does compress calculated fold change values. RMA consists of three steps: 1. Background adjustment 2. Quantile normalization 3. Summarization This is a multi-chip analysis approach. Therefore, all arrays intended for comparison should be included together in the summarization step. For a more detailed description of the RMA algorithm, see the publication, Exploration, Normalization, and Summaries of High Density Oligonucleotide Array Probe Level Data, Biostatistics, April 2003; Vol. 4; Number 2: 249–264.

Notes:

Experiment Type:

This data set includes four experimental conditions, B (baseline, untreated), C (chronic mild stress), CR (chronic mild stress followed by acute restraint), and R (acute restraint only).  B = untreated C = 7 weeks of chronic unpredictable stress R = 30 minutes of restraint CR = 7 weeks of chronic unpredictable stress followed by 30 minutes of restraint

Contributor:

This data set is part of a collaborative effort between UTHSC investigators Byron Jones, Rob Williams, Megan Mulligan, and Lu Lu and collaborators at I.N.R.A Centre de recherche de Toulouse Terenina, Pierre Mormede and Elena Terenina.

Citation:

Data source acknowledgment:

Study Id:

244

• 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)