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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.
Experiment design
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
About cases
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 tissue
This data set includes expression data from mouse hippocampus.
About 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.
Contributors
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.
Specifics of this data set
Z-Score. In general, the array data that we put in GeneNetwork has be logged and then z normalized, but instead of leaving the mean at 0 and the standard deviation of 1 unit, we shift up to a mean of 8 units and increase the spread by having an standard deviation of 2 units (what we call 2Z + 8 normalized data). This removes negative values from the tables.