UTHSC BXD Aged Hippocampus Affy Mouse Gene 1.0 ST (Jun15) RMA **

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Summary

This dataset is now public. Download the dataset and supplementary data files

Experiment design

RNA Extraction and data generation

RNA was extracted using the RNeasy mini kit (Qiagen, Valencia, CA, USA) according to the manufacturers’ procedure. RNA purity and concentration was checked using 260/280 nm absorbance ratio and RNA integrity was analyzed using the Agilent Bioanalyzer 2100 (Agilent Technologies). Samples with RNA Integrity Numbers (RIN values) > 7.5 were run on Affy MoGene1.0 ST at the UTHSC. This array contains 34,700 probe sets that target ∼29,000 well-defined transcripts (RefSeq mRNA isoforms). A single probe set is a collection of about 27 probes that target known exons within a single gene. The multiple probes design provides a more comprehensive coverage of transcripts from a single gene.

About cases

The BXD recombinant inbred strains are derived from crossing the C57BL/6J (B6) and DBA/2J (D2) parental strains and inbreeding for over 20 generations (Taylor et al., 1999; Peirce et al., 2004). A total of 234 individual mice (140 females and 94 males) that come from 71 BXD strains, parental C57BL/6J, DBA/2J and D2B6F1 hybrid are used in this study. These mice were obtained from UTHSC, ORNL, Beth Israel Deaconess or directly from The Jackson. The age for a great majority of mice were between 12 and 28 months (average of 18 months). The animals were sacrificed under saturated isoflurane and brains were removed and placed in RNAlater prior to dissection. Cerebella and olfactory bulbs were removed; brains were hemisected, and both hippocampi were dissected whole in Dr. Lu’s lab. Hippocampal samples are very close to complete (see Lu et al., 2001) but probably include variable amounts of subiculum and fimbria. All procedures were approved by the UTHSC Institutional Animal Care and Use Committee.

Index Sample Strain Sex Age Batch

1 R7264H C57BL/6J_1 M 489 1

2 052008.03 C57BL/6J_2 F 650 2

3 R7289H C57BL/6J_3 M 756 1

4 052008.01 C57BL/6J_4 M 756 2

5 R7269H DBA/2J_1 M 367 1

6 R7185H DBA/2J_2 F 433 1

7 R7301H DBA/2J_3 F 566 1

8 R7265H D2B6F1_1 M 492 1

9 R7304H D2B6F1_2 F 495 1

10 R7276H BXD1_1 M 323 1

11 R7281H BXD1_2 F 448 1

12 051209.20 BXD1_3 F 477 2

13 R7261H BXD2_1 M 394 1

14 R7256H BXD2_2 F 456 1

15 022807.04 BXD2_3 M 483 2

16 042909.46 BXD2_4 M 609 2

17 042909.47 BXD2_5 F 609 2

18 R7223H BXD6_1 M 526 1

19 R7198H BXD8_1 F 433 1

20 R7200H BXD8_2 F 460 1

21 R7203H BXD8_3 M 471 1

22 R7294H BXD9_1 F 456 1

23 052008.17 BXD9_2 M 631 2

24 052008.18 BXD9_3 M 631 2

25 R7300H BXD11_1 M 457 1

26 R7227H BXD11_2 F 536 1

27 021113.01 BXD11_3 F 741 2

28 021113.02 BXD11_4 F 741 2

29 R7183H BXD12_1 F 506 1

30 R7233H BXD12_2 F 561 1

31 R7234H BXD12_3 M 606 1

32 020409.01 BXD12_4 F 850 2

33 020409.03 BXD12_5 M 850 2

34 R7238H BXD14_1 F 605 1

35 R7235H BXD14_2 M 605 1

36 022807.11 BXD16_1 F 455 2

37 R7239H BXD16_2 M 475 1

38 R7236H BXD16_3 F 561 1

39 R7229H BXD18_1 F 493 1

40 020409.28 BXD18_2 F 548 2

41 R7268H BXD19_1 M 492 1

42 R7267H BXD19_2 F 551 1

43 R7263H BXD20_1 M 489 1

44 R7232H BXD20_2 M 506 1

45 R7230H BXD21_1 F 537 1

46 R7260H BXD22_1 F 502 1

47 R7262H BXD22_2 M 596 1

48 020409.08 BXD22_3 F 675 2

49 R7257H BXD23_1 M 462 1

50 R7258H BXD23_2 F 502 1

51 020107.15 BXD23_3 M 512 2

52 R7228H BXD24_1 F 415 1

53 R7255H BXD24_2 F 456 1

54 R7231H BXD24_3 M 470 1

55 020409.21 BXD24_4 F 636 2

56 020409.29 BXD24_5 F 639 2

57 052008.36 BXD25_1 F 430 2

58 R7252H BXD25_2 F 454 1

59 052008.115 BXD25_3 M 709 2

60 R7286H BXD27_1 F 472 1

61 R7170H BXD27_2 F 472 1

62 R7254H BXD28_1 M 493 1

63 R7251H BXD28_2 F 543 1

64 020107.18 BXD28_3 M 605 2

65 R7259H BXD29_1 F 483 1

66 040109.92 BXD31_1 F 445 2

67 031407.18 BXD31_2 F 467 2

68 020409.31 BXD31_3 F 648 2

69 042909.71 BXD32_1 M 566 2

70 R7244H BXD33_1 F 448 1

71 R7253H BXD33_2 M 464 1

72 R7174H BXD33_3 F 471 1

73 R7270H BXD33_4 M 662 1

74 040109.79 BXD33_5 F 683 2

75 050609.35 BXD34_1 F 414 2

76 052008.51 BXD34_2 F 549 2

77 101513.06 BXD34_3 F 554 2

78 101513.07 BXD34_4 F 748 2

79 R7247H BXD38_1 M 446 1

80 R7242H BXD38_3 F 464 1

81 020107.25 BXD38_4 M 530 2

82 R7173H BXD39_1 F 500 1

83 R7175H BXD39_2 M 500 1

84 R7250H BXD39_3 M 536 1

85 020409.19 BXD39_4 F 661 2

86 R7288H BXD40_1 F 451 1

87 051209.56 BXD40_2 F 451 2

88 R7210H BXD40_3 M 470 1

89 R7197H BXD40_4 M 614 1

90 042909.19 BXD40_5 F 633 2

91 020409.73 BXD40_6 F 728 2

92 R7246H BXD42_1 M 446 1

93 R7266H BXD42_2 F 486 1

94 R7280H BXD42_3 F 518 1

95 R7249H BXD43_1 F 454 1

96 R7248H BXD43_2 M 462 1

97 050609.76 BXD43_3 M 616 2

98 R7241H BXD44_1 M 415 1

99 R7279H BXD44_2 M 419 1

100 R7243H BXD44_3 F 438 1

101 042607.13 BXD44_4 F 564 2

102 042607.14 BXD44_5 F 564 2

103 R7176H BXD45_1 F 451 1

104 040109.88 BXD45_2 M 631 2

105 R7245H BXD48_1 F 499 1

106 R7220H BXD48_2 M 526 1

107 051209.29 BXD48_3 M 740 2

108 101513.10 BXD48_4 F 740 2

109 R7299H BXD48a_1 F 479 1

110 R7297H BXD48a_2 M 479 1

111 051209.01 BXD48a_3 F 479 2

112 051209.03 BXD48a_4 M 479 2

113 051209.52 BXD48a_5 F 608 2

114 051209.65 BXD48a_6 M 748 2

115 R7224H BXD50_1 F 530 1

116 R7221H BXD50_2 M 530 1

117 050609.04 BXD50_3 F 778 2

118 R7177H BXD51_1 F 487 1

119 R7290H BXD51_2 M 407 1

120 041709.11 BXD51_3 M 621 2

121 R7222H BXD55_1 M 528 1

122 R7225H BXD55_2 F 587 1

123 052008.134 BXD55_3 F 778 2

124 052008.135 BXD55_4 F 766 2

125 R7178H BXD56_1 M 501 1

126 051209.66 BXD56_2 M 694 2

127 052008.139 BXD56_3 F 734 2

128 042909.52 BXD60_1 M 457 2

129 101513.14 BXD60_2 F 759 2

130 052008.63 BXD61_1 M 650 2

131 020409.14 BXD61_2 F 702 2

132 121214.20 BXD62_1 F 353 2

133 R7291H BXD62_2 M 439 1

134 040109.91 BXD62_3 F 699 2

135 R7218H BXD63_1 M 438 1

136 R7215H BXD63_2 F 475 1

137 050609.28 BXD63_3 M 972 2

138 R7219H BXD64_1 M 528 1

139 R7216H BXD64_2 F 587 1

140 R7217H BXD65_1 F 425 1

141 050609.39 BXD65_2 M 601 2

142 052008.67 BXD65_3 F 808 2

143 R7273H BXD65a_1 F 389 1

144 R7277H BXD65a_2 M 715 1

145 061407.15 BXD65a_3 F 536 2

146 061407.16 BXD65a_4 F 536 2

147 R7271H BXD65b_1 M 483 1

148 R7302H BXD66_1 F 446 1

149 R7214H BXD66_2 M 463 1

150 042507.19 BXD66_3 M 557 2

151 042507.20 BXD66_4 F 557 2

152 R7278H BXD67_1 F 415 1

153 R7213H BXD67_2 M 425 1

154 R7240H BXD67_3 F 499 1

155 042607.11 BXD67_4 F 606 2

156 052008.71 BXD67_5 F 649 2

157 R7211H BXD68_1 F 415 1

158 R7212H BXD68_2 M 421 1

159 042607.27 BXD68_3 F 623 2

160 042607.28 BXD68_4 F 623 2

161 R7305H BXD69_1 F 504 1

162 061913.13 BXD69_2 F 558 2

163 112707.08 BXD69_3 F 602 2

164 R7207H BXD70_1 F 458 1

165 R7204H BXD70_2 M 460 1

166 042909.28 BXD70_3 F 761 2

167 042909.29 BXD70_4 F 761 2

168 R7205H BXD71_1 M 471 1

169 R7208H BXD71_2 F 474 1

170 020409.11 BXD71_3 F 701 2

171 020409.49 BXD71_4 F 582 2

172 R7209H BXD73_1 F 470 1

173 R7206H BXD73_2 M 464 1

174 011007.16 BXD73_3 F 544 2

175 052008.81 BXD73_4 F 642 2

176 R7181H BXD73a_1 F 443 1

177 061407.18 BXD73a_2 F 443 2

178 R7182H BXD73a_3 M 614 1

179 052008.86 BXD73a_4 M 710 2

180 031407.10 BXD74_1 M 804 2

181 011107.08 BXD75_1 F 535 2

182 R7188H BXD76_1 F 408 1

183 R7187H BXD76_2 M 564 1

184 R7179H BXD76_3 M 579 1

185 R7292HR BXD77_1 M 347 1

186 R7201H BXD77_2 F 454 1

187 052008.83 BXD77_3 F 659 2

188 R7202H BXD79_1 M 485 1

189 R7199H BXD79_2 F 515 1

190 R7298H BXD79_3 M 704 1

191 050609.25 BXD81_1 F 434 2

192 R7190H BXD81_2 F 458 1

193 R7196H BXD81_3 M 515 1

194 R7184H BXD83_1 M 441 1

195 061307.30 BXD83_2 F 612 2

196 121907.10 BXD83_3 M 617 2

197 R7195H BXD84_1 M 474 1

198 R7296H BXD84_2 M 484 1

199 R7192H BXD84_3 F 522 1

200 020409.80 BXD84_4 F 564 2

201 112707.12 BXD84_5 F 592 2

202 R7272H BXD85_1 M 425 1

203 R7193H BXD85_2 F 506 1

204 020409.12 BXD85_3 F 702 2

205 020409.13 BXD85_4 F 702 2

206 R7191H BXD86_1 M 425 1

207 020409.35 BXD86_2 F 613 2

208 020409.36 BXD86_3 F 613 2

209 R7194H BXD87_1 F 425 1

210 R7303HR BXD87_2 M 478 1

211 R7186H BXD87_3 M 442 1

212 052008.97 BXD87_4 F 666 2

213 052008.98 BXD87_5 M 666 2

214 R7295H BXD89_1 F 446 1

215 052008.100 BXD89_2 M 616 2

216 R7287H BXD90_1 M 434 1

217 R7293H BXD90_2 M 558 1

218 052008.105 BXD90_3 F 452 2

219 R7180H BXD95_1 F 467 1

220 R7169H BXD95_2 M 467 1

221 100914.09 BXD95_3 F 536 2

222 R7237H BXD98_1 M 605 1

223 R7171H BXD98_2 F 639 1

224 R7275H BXD98_3 F 488 1

225 R7189H BXD99_1 M 524 1

226 R7172H BXD99_2 F 471 1

227 R7282H BXD100_1 F 463 1

228 R7283H BXD100_2 M 507 1

229 R7274H BXD100_3 M 577 1

230 R7226H BXD100_4 F 464 1

231 051209.62 BXD100_5 M 577 2

232 R7284H BXD101_1 F 490 1

233 R7285H BXD101_2 M 408 1

234 051112.10 BXD101_3 F 223 2

About data processing

Probe set level intensity values were extracted from the CEL files using the Affymetrix GeneChip Operating Software. Data normalization was performed using the R package “Affy” available from www.Bioconductor.org. The Robust Multichip Averaging protocol was used to process the expression values. The array data was then log transformed and rescaled using a z-scoring procedure to set the mean of each sample at eight expression units with a SD of 2 units.

Specifics of this data set

Gene Level