From b2feda451ccfbeaed02dce9088d6dd228cf15861 Mon Sep 17 00:00:00 2001 From: Bonface Date: Tue, 13 Feb 2024 23:52:26 -0600 Subject: Update dataset RTF Files. --- .../Devstriatum_ilm6_2p3rinv_1111/cases.rtf | 1 + .../experiment-design.rtf | 1 + .../Devstriatum_ilm6_2p3rinv_1111/processing.rtf | 1 + .../Devstriatum_ilm6_2p3rinv_1111/summary.rtf | 10 + .../Devstriatum_ilm6_2p3rinv_1111/tissue.rtf | 534 +++++++++++++++++++++ 5 files changed, 547 insertions(+) create mode 100644 general/datasets/Devstriatum_ilm6_2p3rinv_1111/cases.rtf create mode 100644 general/datasets/Devstriatum_ilm6_2p3rinv_1111/experiment-design.rtf create mode 100644 general/datasets/Devstriatum_ilm6_2p3rinv_1111/processing.rtf create mode 100644 general/datasets/Devstriatum_ilm6_2p3rinv_1111/summary.rtf create mode 100644 general/datasets/Devstriatum_ilm6_2p3rinv_1111/tissue.rtf (limited to 'general/datasets/Devstriatum_ilm6_2p3rinv_1111') diff --git a/general/datasets/Devstriatum_ilm6_2p3rinv_1111/cases.rtf b/general/datasets/Devstriatum_ilm6_2p3rinv_1111/cases.rtf new file mode 100644 index 0000000..74c0f5e --- /dev/null +++ b/general/datasets/Devstriatum_ilm6_2p3rinv_1111/cases.rtf @@ -0,0 +1 @@ +

The BXD genetic reference panel of recombinant inbred strains consists of just over 80 strains. The BXDs in this data set include 28 of the BXD strains made by Benjamin Taylor at the Jackson Laboratory in the 1970s and 1990s (BXD1 through BXD42). All of these strains are fully inbred, many well beyond the 100th filial (F) generation of inbreeding. We have also included 4 new inbred strains BXD (F21+) generated by Lu and Peirce. All of these strains were been genotyped at 13,377 SNPs in 2005 (Shifman et al., 2006).

diff --git a/general/datasets/Devstriatum_ilm6_2p3rinv_1111/experiment-design.rtf b/general/datasets/Devstriatum_ilm6_2p3rinv_1111/experiment-design.rtf new file mode 100644 index 0000000..cfea6b0 --- /dev/null +++ b/general/datasets/Devstriatum_ilm6_2p3rinv_1111/experiment-design.rtf @@ -0,0 +1 @@ +

This data set consists arrays processed in 8 groups over a 2 month period (from July-August 2010). All groups consisted of 24 samples. All arrays in this data set were processed using a single protocol by a single operator. Processing was supervised directly by Lorne Rose. All samples were scanned on a single Illumina Beadstation housed in the Hamilton Eye Institute between Month Day and Month Day, Year. Details on sample assignment to slides and batches is provide in the table below.

diff --git a/general/datasets/Devstriatum_ilm6_2p3rinv_1111/processing.rtf b/general/datasets/Devstriatum_ilm6_2p3rinv_1111/processing.rtf new file mode 100644 index 0000000..aee498f --- /dev/null +++ b/general/datasets/Devstriatum_ilm6_2p3rinv_1111/processing.rtf @@ -0,0 +1 @@ +

Samples were processed by Lorne Rose and colleagues in the Illumina Core at UTHSC between July and August 2010. In brief, RNA purity was evaluated using the 260/280 nm absorbance ratio, and values had to be greater than 1.8 to pass our quality control (QC). The majority of samples had values between 1.9 and 2.1. RNA integrity was assessed using the Agilent Bioanalyzer 2100. The standard Eberwine T7 polymerase method was used to catalyze the synthesis of cDNA template from polyA-tailed RNA using the Ambion/Illumina (http://www.ambion.com/catalog/CatNum.php?AMIL1791) TotalPrep RNA amplication kit (Cat IL1791). The biotin labeled cRNA was then evaluated using both the 260/280 ratio (values of 2.0-2.3 are acceptable) using a NanoDrop ND-1000 (http://www.nanodrop.com/nd-1000-overview.html). Those samples that passed QC steps (1-3% failed and new RNA samples had to be acquired and processed) were immediately used on Mouse-6 v 1.1 slide. The slides were hybridized and washed following standard Illumina protocols.

diff --git a/general/datasets/Devstriatum_ilm6_2p3rinv_1111/summary.rtf b/general/datasets/Devstriatum_ilm6_2p3rinv_1111/summary.rtf new file mode 100644 index 0000000..3515533 --- /dev/null +++ b/general/datasets/Devstriatum_ilm6_2p3rinv_1111/summary.rtf @@ -0,0 +1,10 @@ +

The BIDMC/UTHSC Dev Striatum P3 ILMv6.2 (Nov10) RankInv ** data set provides estimates of mRNA expression during two developmental ages (postnatal days 3 and 14) in the cerebral cortex from 32 BXD strains. All samples are from normal animals raised and bred in a standard laboratory environment.

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All samples were processed using 32 Illumina Sentrix v6.2 BeadArray slides. All samples passed stringent quality control and error checking. This data set is a companion to the BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov10) RankInv ** data set and was processed using identical methods and the same strains. This data set was processed using the Illumina "Rank Invariant" protocol. Values were log2 transformed and the current data range from XXX (very low or no expression) to XXXX (extremely high).

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As a measure of data quality we often count the number of probes that are associated with LOD scores of greater than 10 (LRS > 46). In this data set, xxxx probes have LRS values >46 (LOD >10).

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Users of these mouse striatum data set may also find the following complementary resources and papers useful:

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A movie of the dissection of the brain by Dr. Glenn Rosen. www.rosenlab.net/Movie/P3.mov
+www.rosenlab.net/Movie/P14.mov

diff --git a/general/datasets/Devstriatum_ilm6_2p3rinv_1111/tissue.rtf b/general/datasets/Devstriatum_ilm6_2p3rinv_1111/tissue.rtf new file mode 100644 index 0000000..e9e6151 --- /dev/null +++ b/general/datasets/Devstriatum_ilm6_2p3rinv_1111/tissue.rtf @@ -0,0 +1,534 @@ +

All animals were raised at Beth Israel Deaconess Medical Center in SPF facilities from stock obtained from either Jackson Laboratory or UTHSC. All mice were killed by decapitation. Whole brain dissections were performed at Beth Israel Deaconess Medical Center by Glenn Rosen and colleagues. Care was taken to assure that samples were comprised of the dorsal striatum, although it is possible that ventral striatum (accumbens) was occasionally included.

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All animals used in this study were either 3 or 14 days of age. A pool of dissected striatal tissue from three naive animals of the same strain and age were collected in one session and used to generate RNA samples. The great majority (75%) of animals were sacrificed between 9:30 AM and 11:30 AM. All animals were sacrificed between 9 AM and 5 PM during the light phase. All RNA samples were extracted at Beth Israel Deaconess Medical Center by Glenn Rosen and colleagues.

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IndexStrainAgeBatch IDSample IDTube ID
1BXD1P385237939012_A232
2BXD1P315448576016_C234
3BXD2P375384138020_C230
4BXD2P365384138053_A228
5BXD5P365384138053_D270
6BXD5P355452241004_E268
7BXD6P325384138018_A102
8BXD6P315448576016_A101
9BXD8P335384138048_B110
10BXD9P325384138041_A280
11BXD9P335384138058_C278
12BXD11P325384138018_B121
13BXD11P335384138048_C123
14BXD12P355452241004_A127
15BXD12P345452241007_B125
16BXD13P385237939010_D181
17BXD13P315448576016_B183
18BXD14P355452241017_A420
19BXD14P345452241023_C419
20BXD15P375384138016_C475
21BXD15P385448576010_F476
22BXD16P365384138009_F204
23BXD16P375384138020_D205
24BXD18P375384138017_B388
25BXD18P335452241008_B385
26BXD19P325384138018_E212
27BXD19P335384138048_F213
28BXD20P325384138047_C431
29BXD20P315448576029_A431
30BXD21P355452241006_A311
31BXD21P345452241022_E309
32BXD24aP365384138053_B247
33BXD24aP345452241022_B244
34BXD27P375384138021_D294
35BXD27P365384138053_E293
36BXD28P375384138016_F543
37BXD28P385448576011_B545
38BXD29P375384138016_D495
39BXD29P385448576011_A498
40BXD31P345452241031_D577
41BXD31P335452241034_D575
42BXD32P355452241006_E402
43BXD32P345452241023_B401
44BXD34P325384138041_D348
45BXD34P315448576016_E347
46BXD36P325384138047_B417
47BXD36P335452241008_D418
48BXD38P385237939012_E321
49BXD38P315448576016_D322
50BXD39P355452241017_F511
51BXD39P345452241031_A512
52BXD40P385448576010_B368
53BXD40P315448576016_F371
54BXD42P325384138047_E481
55BXD42P315448576029_C479
56BXD51P345452241031_F616
57BXD51P335452241034_F615
58BXD61P355452241024_C555
59BXD61P365452241035_B557
60BXD70P375384138017_E584
61BXD70P385448576011_D585
62BXD73P355452241024_E600
63BXD73P365452241035_E601
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