BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov10) RankInv ** modify this page

Accession number: GN274

Summary:

IN PROGRESS: Data generated by Dr. Glenn D. Rosen and colleagues

The Neocortex Developmental 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.

Some of these data were used in
Gaglani SM, Lu L, Williams RW, Rosen GD (2009) The genetic control of neocortex volume and covariation with patterns of gene expression in mice. BMC Neuroscience 10:44 Full Text HTML Version, Full Text PDF Version

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 Striatal Developmental Transcriptome 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).

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 Neocortex Developmental data set, xxxx probes have LRS values >46 (LOD >10).

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

Rossner and colleagues, 2006: a paper on the transcriptome of identified subtypes of neurons in the mouse neocortex.

A movie of the dissection of the brain by Dr. Glenn Rosen. ABOUT THE NEOCORTEX

About the strains used to generate this set of data

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).

Animals and Tissue Used to Generate This Set of Data:

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. Neocortex samples were close to complete but are likely to include variable amounts of underlying white matter. Samples may also include parts of the pyriform cortex and subiculum.

All animals used in this study were either 3 or 14 days of age. A pool of dissected neocortical 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 D. Rosen and colleagues.

IndexStrainAgeBatch IDSample IDTube ID
1BXD1P325384138018_F236
2BXD1P335384138058_A239
3BXD2P325384138018_C168
4BXD2P315448576044_F167
5BXD5P375384138020_A273
6BXD5P345452241022_C267
7BXD6P335384138048_A107
8BXD6P345452241007_A108
9BXD8P365384138009_A113
10BXD8P375384138021_C115
11BXD9P355452241004_F289
12BXD9P345452241022_D288
13BXD11P385237939010_A117
14BXD11P315448576044_D120
15BXD12P365384138009_B130
16BXD12P375384138021_B132
17BXD13P375384138020_F161
18BXD13P355452241004_C164
19BXD14P355452241004_B158
20BXD14P365452241033_D424
21BXD15P335452241008_C437
22BXD15P345452241023_D438
23BXD16P335384138048_D170
24BXD16P345452241007_D172
25BXD18P385448576010_A390
26BXD18P315448576045_E392
27BXD19P385237939010_E210
28BXD19P315448576045_A211
29BXD20P355452241017_B439
30BXD20P365452241033_E441
31BXD21P375384138021_F341
32BXD21P365384138053_F315
33BXD24aP385237939012_B251
34BXD24aP375384138020_B250
35BXD27P385237939012_D298
36BXD27P315448576045_C300
37BXD28P325384138049_B550
38BXD28P315448576029_F548
39BXD29P325384138047_F502
40BXD29P315448576029_D501
41BXD31P355452241024_D579
42BXD31P365452241035_D582
43BXD32P355452241006_F407
44BXD32P365452241033_C408
45BXD34P385237939012_F345
46BXD34P345452241022_F355
47BXD36P375384138016_A429
48BXD36P385448576010_D430
49BXD38P325384138041_F327
50BXD38P335384138058_E328
51BXD39P375384138016_E515
52BXD39P355452241024_A518
53BXD40P325384138041_C373
54BXD40P335452241008_A375
55BXD42P335452241008_E485
56BXD42P345452241023_F486
57BXD51P355452241024_F621
58BXD51P365452241035_F622
59BXD61P345452241031_C554
60BXD61P335452241034_A552
61BXD70P325384138049_D590
62BXD70P315448576044_B589
63BXD73P325384138049_E603
64BXD73P385448576011_E605

Sample Processing:

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.

Experimental Design and Batch Structure:

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.

Data Source Acknowledgements: