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Experiment design
RNA Extraction
RNA was extracted using the RNeasy mini kit (Qiagen, Valencia, CA, USA) according to the manufacturers’ procedure. 2100 BioAnalyzer (Agilent Technologies) was used to evaluate RNA integrity and quality. Samples with RNA Integrity Numbers (RIN values) > 8.0 were run on Affy MoGene1.0 ST at the UTHSC.
About cases
The study included 97 mice (12~32-month-old except 1 BXD101 mouse) from C57BL/6J and 56 BXD strains. All procedures were approved by the UTHSC Institutional Animal Care and Use Committee.
The table of samples that are finally used for this study.
|
Index |
Sample ID |
Case ID |
Strain |
Sex |
Age |
Tissue |
|
1 |
A46 |
051209.20 |
BXD1 |
F |
477 |
Hippocampus |
|
2 |
A36 |
042909.47 |
BXD2 |
F |
609 |
Hippocampus |
|
3 |
A35 |
042909.46 |
BXD2 |
M |
609 |
Hippocampus |
|
4 |
A50 |
022807.04 |
BXD2 |
M |
483 |
Hippocampus |
|
5 |
A54 |
052008.18 |
BXD9 |
F |
631 |
Hippocampus |
|
6 |
A53 |
052008.17 |
BXD9 |
M |
631 |
Hippocampus |
|
7 |
A16B |
021113.01 |
BXD11 |
F |
741 |
Hippocampus |
|
8 |
A17B |
021113.02 |
BXD11 |
F |
741 |
Hippocampus |
|
9 |
A14 |
020409.01 |
BXD12 |
F |
850 |
Hippocampus |
|
10 |
A13 |
020409.03 |
BXD12 |
M |
850 |
Hippocampus |
|
11 |
A51 |
022807.11 |
BXD16 |
F |
455 |
Hippocampus |
|
12 |
A10 |
020409.28 |
BXD18 |
F |
548 |
Hippocampus |
|
13 |
A6 |
020409.08 |
BXD22 |
F |
675 |
Hippocampus |
|
14 |
A49 |
020107.15 |
BXD23 |
M |
512 |
Hippocampus |
|
15 |
A8 |
020409.21 |
BXD24 |
F |
636 |
Hippocampus |
|
16 |
A9 |
020409.29 |
BXD24 |
F |
639 |
Hippocampus |
|
17 |
A55 |
052008.36 |
BXD25 |
F |
430 |
Hippocampus |
|
18 |
A67 |
052008.115 |
BXD25 |
M |
709 |
Hippocampus |
|
19 |
A20 |
020107.18 |
BXD28 |
M |
605 |
Hippocampus |
|
20 |
A24 |
040109.92 |
BXD31 |
F |
445 |
Hippocampus |
|
21 |
A7 |
020409.31 |
BXD31 |
F |
648 |
Hippocampus |
|
22 |
A79 |
031407.18 |
BXD31 |
F |
467 |
Hippocampus |
|
23 |
A32 |
042909.71 |
BXD32 |
M |
566 |
Hippocampus |
|
24 |
A26 |
040109.79 |
BXD33 |
F |
683 |
Hippocampus |
|
25 |
A101 |
050609.35 |
BXD34 |
F |
414 |
Hippocampus |
|
26 |
A56 |
052008.51 |
BXD34 |
F |
549 |
Hippocampus |
|
27 |
A90B |
101513.06 |
BXD34 |
F |
554 |
Hippocampus |
|
28 |
A90B2 |
101513.07 |
BXD34 |
F |
748 |
Hippocampus |
|
29 |
A47 |
020107.25 |
BXD38 |
M |
530 |
Hippocampus |
|
30 |
A5 |
020409.19 |
BXD39 |
F |
661 |
Hippocampus |
|
31 |
A105 |
051209.56 |
BXD40 |
F |
451 |
Hippocampus |
|
32 |
A39 |
020409.73 |
BXD40 |
F |
728 |
Hippocampus |
|
33 |
A40 |
042909.19 |
BXD40 |
F |
633 |
Hippocampus |
|
34 |
A99 |
050609.76 |
BXD43 |
M |
616 |
Hippocampus |
|
35 |
A74 |
042607.13 |
BXD44 |
F |
564 |
Hippocampus |
|
36 |
A75 |
042607.14 |
BXD44 |
F |
564 |
Hippocampus |
|
37 |
A23 |
040109.88 |
BXD45 |
M |
631 |
Hippocampus |
|
38 |
A100B |
101513.10 |
BXD48 |
F |
740 |
Hippocampus |
|
39 |
A45 |
051209.29 |
BXD48 |
M |
740 |
Hippocampus |
|
40 |
A93 |
050609.04 |
BXD50 |
F |
778 |
Hippocampus |
|
41 |
A92 |
041709.11 |
BXD51 |
M |
621 |
Hippocampus |
|
42 |
A68 |
052008.134 |
BXD55 |
F |
778 |
Hippocampus |
|
43 |
A69 |
052008.135 |
BXD55 |
F |
766 |
Hippocampus |
|
44 |
A70 |
052008.139 |
BXD56 |
F |
734 |
Hippocampus |
|
45 |
A42 |
051209.66 |
BXD56 |
M |
694 |
Hippocampus |
|
46 |
A4B |
101513.14 |
BXD60 |
F |
759 |
Hippocampus |
|
47 |
A33 |
042909.52 |
BXD60 |
M |
457 |
Hippocampus |
|
48 |
A11 |
020409.14 |
BXD61 |
F |
702 |
Hippocampus |
|
49 |
A57 |
052008.63 |
BXD61 |
M |
650 |
Hippocampus |
|
50 |
A106B |
121214.20 |
BXD62 |
F |
353 |
Hippocampus |
|
51 |
A21 |
040109.91 |
BXD62 |
F |
699 |
Hippocampus |
|
52 |
A98 |
050609.28 |
BXD63 |
M |
972 |
Hippocampus |
|
53 |
A58 |
052008.67 |
BXD65 |
F |
808 |
Hippocampus |
|
54 |
A97 |
050609.39 |
BXD65 |
M |
601 |
Hippocampus |
|
55 |
A72 |
042507.19 |
BXD66 |
F |
557 |
Hippocampus |
|
56 |
A73 |
042507.20 |
BXD66 |
F |
557 |
Hippocampus |
|
57 |
A59 |
052008.71 |
BXD67 |
F |
649 |
Hippocampus |
|
58 |
A71 |
042607.11 |
BXD67 |
F |
606 |
Hippocampus |
|
59 |
A76 |
042607.27 |
BXD68 |
F |
623 |
Hippocampus |
|
60 |
A77 |
042607.28 |
BXD68 |
F |
623 |
Hippocampus |
|
61 |
A27B |
061913.13 |
BXD69 |
F |
558 |
Hippocampus |
|
62 |
A86 |
112707.08 |
BXD69 |
F |
602 |
Hippocampus |
|
63 |
A37 |
042909.28 |
BXD70 |
F |
761 |
Hippocampus |
|
64 |
A38 |
042909.29 |
BXD70 |
F |
761 |
Hippocampus |
|
65 |
A12 |
020409.11 |
BXD71 |
F |
701 |
Hippocampus |
|
66 |
A2 |
020409.49 |
BXD71 |
F |
582 |
Hippocampus |
|
67 |
A60 |
052008.81 |
BXD73 |
F |
642 |
Hippocampus |
|
68 |
A81 |
011007.16 |
BXD73 |
F |
544 |
Hippocampus |
|
69 |
A78 |
031407.10 |
BXD74 |
M |
804 |
Hippocampus |
|
70 |
A80 |
011107.08 |
BXD75 |
F |
535 |
Hippocampus |
|
71 |
A61 |
052008.83 |
BXD77 |
F |
659 |
Hippocampus |
|
72 |
A84 |
061407.18 |
BXD80 |
F |
443 |
Hippocampus |
|
73 |
A62 |
052008.86 |
BXD80 |
M |
710 |
Hippocampus |
|
74 |
A96 |
050609.25 |
BXD81 |
F |
434 |
Hippocampus |
|
75 |
A48 |
061307.30 |
BXD83 |
F |
612 |
Hippocampus |
|
76 |
A85 |
121907.10 |
BXD83 |
M |
617 |
Hippocampus |
|
77 |
A34 |
020409.80 |
BXD84 |
F |
564 |
Hippocampus |
|
78 |
A87 |
112707.12 |
BXD84 |
F |
592 |
Hippocampus |
|
79 |
A25 |
020409.12 |
BXD85 |
F |
702 |
Hippocampus |
|
80 |
A31 |
020409.13 |
BXD85 |
F |
702 |
Hippocampus |
|
81 |
A1 |
020409.35 |
BXD86 |
F |
613 |
Hippocampus |
|
82 |
A15 |
020409.36 |
BXD86 |
F |
613 |
Hippocampus |
|
83 |
A63 |
052008.97 |
BXD87 |
F |
666 |
Hippocampus |
|
84 |
A64 |
052008.98 |
BXD87 |
M |
666 |
Hippocampus |
|
85 |
A65 |
052008.100 |
BXD89 |
M |
616 |
Hippocampus |
|
86 |
A66 |
052008.105 |
BXD90 |
F |
452 |
Hippocampus |
|
87 |
A44B |
100914.09 |
BXD95 |
F |
536 |
Hippocampus |
|
88 |
A107 |
051209.01 |
BXD96 |
F |
479 |
Hippocampus |
|
89 |
A43 |
051209.52 |
BXD96 |
F |
608 |
Hippocampus |
|
90 |
A104 |
051209.03 |
BXD96 |
M |
479 |
Hippocampus |
|
91 |
A41 |
051209.65 |
BXD96 |
M |
748 |
Hippocampus |
|
92 |
A82 |
061407.15 |
BXD97 |
F |
536 |
Hippocampus |
|
93 |
A83 |
061407.16 |
BXD97 |
F |
536 |
Hippocampus |
|
94 |
A108 |
051209.62 |
BXD100 |
M |
577 |
Hippocampus |
|
95 |
A30B |
051112.10 |
BXD101 |
F |
223 |
Hippocampus |
|
96 |
A52 |
052008.03 |
C57BL/6J |
F |
650 |
Hippocampus |
|
97 |
A103 |
052008.01 |
C57BL/6J |
M |
756 |
Hippocampus |
About tissue
Tissue Harvest
The animals were sacrificed under saturated isoflurane. The hippocampus from the animals was dissected and stored at −80°C until RNA extraction.
About data processing
Raw microarray data were normalized using the Robust Multichip Array (RMA) method. The expression data were then re-normalized using a modified Z score.