From d029d5d7f8ead1f1de8d318045004a4a6f68f5fb Mon Sep 17 00:00:00 2001 From: Bonface Date: Fri, 9 Feb 2024 09:41:28 -0600 Subject: Update dataset RTF Files. --- general/datasets/UTHSC_BXD_HArev3_0912/cases.rtf | 1258 ++++++++++++++++++++ .../UTHSC_BXD_HArev3_0912/experiment-design.rtf | 3 + .../datasets/UTHSC_BXD_HArev3_0912/processing.rtf | 3 + general/datasets/UTHSC_BXD_HArev3_0912/tissue.rtf | 3 + 4 files changed, 1267 insertions(+) create mode 100644 general/datasets/UTHSC_BXD_HArev3_0912/cases.rtf create mode 100644 general/datasets/UTHSC_BXD_HArev3_0912/experiment-design.rtf create mode 100644 general/datasets/UTHSC_BXD_HArev3_0912/processing.rtf create mode 100644 general/datasets/UTHSC_BXD_HArev3_0912/tissue.rtf (limited to 'general/datasets/UTHSC_BXD_HArev3_0912') diff --git a/general/datasets/UTHSC_BXD_HArev3_0912/cases.rtf b/general/datasets/UTHSC_BXD_HArev3_0912/cases.rtf new file mode 100644 index 0000000..2b37c95 --- /dev/null +++ b/general/datasets/UTHSC_BXD_HArev3_0912/cases.rtf @@ -0,0 +1,1258 @@ +

The study includes 137 mice (11~25 months old) from 73 strains (B6, D2, DBF1, and 70 BXD strains). All procedures were approved by the UTHSC Institutional Animal Care and Use Committee.

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The table of samples that are finally used for this study:

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
IndexStrainSexRNA IDAgePhaseTissue
1BXD1FR7281H448IIHippocampus
2BXD1MR7276H323IIHippocampus
3BXD2MR7261H394IHippocampus
4BXD2FR7256H456IHippocampus
5BXD6MR7223H526IHippocampus
6BXD8MR7203H471IHippocampus
7BXD8FR7200H460IHippocampus
8BXD8FR7198H433IHippocampus
9BXD9FR7294H456IIHippocampus
10BXD11MR7300H457IIHippocampus
11BXD11FR7227H536IHippocampus
12BXD12FR7183H506IHippocampus
13BXD12FR7233H561IHippocampus
14BXD12MR7234H606IHippocampus
15BXD14FR7238H605IHippocampus
16BXD14MR7235H605IHippocampus
17BXD16FR7236H561IHippocampus
18BXD16MR7239H475IHippocampus
19BXD18FR7229H493IHippocampus
20BXD19FR7267H551IHippocampus
21BXD19MR7268H492IHippocampus
22BXD20MR7232H506IHippocampus
23BXD20MR7263H489IHippocampus
24BXD21FR7230H537IHippocampus
25BXD22FR7260H502IHippocampus
26BXD22MR7262H596IHippocampus
27BXD23FR7258H502IHippocampus
28BXD23MR7257H462IHippocampus
29BXD24MR7231H470IHippocampus
30BXD24FR7228H415IHippocampus
31BXD24FR7255H456IHippocampus
32BXD25FR7252H454IHippocampus
33BXD27FR7286H472IIHippocampus
34BXD27FR7170H472IHippocampus
35BXD28MR7254H493IHippocampus
36BXD28FR7251H543IHippocampus
37BXD29FR7259H483IHippocampus
38BXD33MR7253H464IHippocampus
39BXD33FR7174H471IHippocampus
40BXD33FR7244H448IHippocampus
41BXD33MR7270H662IHippocampus
42BXD38FR7242H464IHippocampus
43BXD38MR7247H446IHippocampus
44BXD39MR7250H536IHippocampus
45BXD39FR7173H500IHippocampus
46BXD39MR7175H500IHippocampus
47BXD40FR7288H451IIHippocampus
48BXD40MR7210H470IHippocampus
49BXD40MR7197H614IHippocampus
50BXD42FR7280H518IIHippocampus
51BXD42MR7246H446IHippocampus
52BXD42FR7266H486IHippocampus
53BXD43FR7249H454IHippocampus
54BXD43MR7248H462IHippocampus
55BXD44MR7241H415IHippocampus
56BXD44MR7279H419IIHippocampus
57BXD44FR7243H438IHippocampus
58BXD45FR7176H451IHippocampus
59BXD48FR7245H499IHippocampus
60BXD48MR7220H526IHippocampus
61BXD48aFR7299H479IIHippocampus
62BXD48aMR7297H479IIHippocampus
63BXD50FR7224H530IHippocampus
64BXD50MR7221H530IHippocampus
65BXD51FR7177H487IHippocampus
66BXD51MR7290H407IIHippocampus
67BXD55MR7222H528IHippocampus
68BXD55FR7225H587IHippocampus
69BXD56MR7178H501IHippocampus
70BXD62MR7291H439IIHippocampus
71BXD63MR7218H438IHippocampus
72BXD63FR7215H475IHippocampus
73BXD64MR7219H528IHippocampus
74BXD64FR7216H587IHippocampus
75BXD65FR7217H425IHippocampus
76BXD65aFR7273H389IIHippocampus
77BXD65aMR7277H715IIHippocampus
78BXD65bMR7271H483IIHippocampus
79BXD66MR7214H463IHippocampus
80BXD66FR7302H446IIIHippocampus
81BXD67FR7240H499IHippocampus
82BXD67MR7213H425IHippocampus
83BXD67FR7278H415IIHippocampus
84BXD68MR7212H421IHippocampus
85BXD68FR7211H415IHippocampus
86BXD69FR7305H504IIIHippocampus
87BXD70FR7207H458IHippocampus
88BXD70MR7204H460IHippocampus
89BXD71MR7205H471IHippocampus
90BXD71FR7208H474IHippocampus
91BXD73FR7209H470IHippocampus
92BXD73MR7206H464IHippocampus
93BXD73aFR7181H443IHippocampus
94BXD73aMR7182H614IHippocampus
95BXD76MR7179H579IHippocampus
96BXD76FR7188H408IHippocampus
97BXD76MR7187H564IHippocampus
98BXD77MR7292H347IIHippocampus
99BXD77FR7201H454IHippocampus
100BXD79MR7202H485IHippocampus
101BXD79FR7199H515IHippocampus
102BXD79MR7298H704IIHippocampus
103BXD81MR7196H515IHippocampus
104BXD81FR7190H458IHippocampus
105BXD83MR7184H441IHippocampus
106BXD84MR7195H474IHippocampus
107BXD84MR7296H484IIHippocampus
108BXD84FR7192H522IHippocampus
109BXD85MR7272H425IIHippocampus
110BXD85FR7193H506IHippocampus
111BXD86MR7191H425IHippocampus
112BXD87FR7194H425IHippocampus
113BXD87MR7303H478IIIHippocampus
114BXD87MR7186H442IHippocampus
115BXD89FR7295H446IIHippocampus
116BXD90MR7287H434IIHippocampus
117BXD90MR7293H558IIHippocampus
118BXD95FR7180H467IHippocampus
119BXD95MR7169H467IHippocampus
120BXD98MR7237H605IHippocampus
121BXD98FR7171H639IHippocampus
122BXD98FR7275H488IIHippocampus
123BXD99MR7189H524IHippocampus
124BXD99FR7172H471IHippocampus
125BXD100FR7282H463IIHippocampus
126BXD100MR7283H507IIHippocampus
127BXD100MR7274H577IIHippocampus
128BXD100FR7226H464IHippocampus
129BXD101FR7284H490IIHippocampus
130BXD101MR7285H408IIHippocampus
131C57BL/6JMR7264H489IHippocampus
132C57BL/6JMR7289H756IIHippocampus
133D2B6F1MR7265H492IHippocampus
134D2B6F1FR7304H495IIIHippocampus
135DBA/2JFR7185H433IHippocampus
136DBA/2JMR7269H367IHippocampus
137DBA/2JFR7301H566IIIHippocampus
diff --git a/general/datasets/UTHSC_BXD_HArev3_0912/experiment-design.rtf b/general/datasets/UTHSC_BXD_HArev3_0912/experiment-design.rtf new file mode 100644 index 0000000..d6b2d5b --- /dev/null +++ b/general/datasets/UTHSC_BXD_HArev3_0912/experiment-design.rtf @@ -0,0 +1,3 @@ +

RNA Extraction

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RNA was extracted using the RNeasy mini kit (Qiagen, Valencia, CA, USA) according to the manufactures’ 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

diff --git a/general/datasets/UTHSC_BXD_HArev3_0912/processing.rtf b/general/datasets/UTHSC_BXD_HArev3_0912/processing.rtf new file mode 100644 index 0000000..e951515 --- /dev/null +++ b/general/datasets/UTHSC_BXD_HArev3_0912/processing.rtf @@ -0,0 +1,3 @@ +

About data processing:

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Raw microarray data were normalized using the Robust Multichip Array (RMA) method. The expression data were then re-normalized using a modified Z score.

diff --git a/general/datasets/UTHSC_BXD_HArev3_0912/tissue.rtf b/general/datasets/UTHSC_BXD_HArev3_0912/tissue.rtf new file mode 100644 index 0000000..3166717 --- /dev/null +++ b/general/datasets/UTHSC_BXD_HArev3_0912/tissue.rtf @@ -0,0 +1,3 @@ +

Tissue Harvest 

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The animals were sacrificed under saturated isoflurane. Hippocampus from the animals were dissected and stored at −80°C until RNA extraction. 

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