Data Set Group2: BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov10)

Data Set: BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov10) RankInv GN Accession: GN275 GEO Series: Title: The genetic control of neocortex volume and covariation with patterns of gene expression in mice. Organism: Mouse (Mus musculus, mm10) Group: BXD Tissue: Neocortex mRNA Dataset Status: Public Platforms: Illumina Mouse WG-6 v2.0 (GPL6887) Normalization: RankInv

Contact Information Glenn Rosen Beth Israel Deaconess Medical Center 330 Brookline Ave. Boston, MA 2215 USA Tel. 617 735-2870 grosen@bidmc.harvard.edu Website Download datasets and supplementary data files GN275_MeanDataAnnotated_rev081815.txt (N/A) GN275_StdError_rev081815.txt (N/A)

Specifics of this Data Set:

None

Summary:

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 cases used to generate this set of data:

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).

About the 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. Index Strain Age Batch ID Sample ID Tube ID 1 BXD1 P3 2 5384138018_F 236 2 BXD1 P3 3 5384138058_A 239 3 BXD2 P3 2 5384138018_C 168 4 BXD2 P3 1 5448576044_F 167 5 BXD5 P3 7 5384138020_A 273 6 BXD5 P3 4 5452241022_C 267 7 BXD6 P3 3 5384138048_A 107 8 BXD6 P3 4 5452241007_A 108 9 BXD8 P3 6 5384138009_A 113 10 BXD8 P3 7 5384138021_C 115 11 BXD9 P3 5 5452241004_F 289 12 BXD9 P3 4 5452241022_D 288 13 BXD11 P3 8 5237939010_A 117 14 BXD11 P3 1 5448576044_D 120 15 BXD12 P3 6 5384138009_B 130 16 BXD12 P3 7 5384138021_B 132 17 BXD13 P3 7 5384138020_F 161 18 BXD13 P3 5 5452241004_C 164 19 BXD14 P3 5 5452241004_B 158 20 BXD14 P3 6 5452241033_D 424 21 BXD15 P3 3 5452241008_C 437 22 BXD15 P3 4 5452241023_D 438 23 BXD16 P3 3 5384138048_D 170 24 BXD16 P3 4 5452241007_D 172 25 BXD18 P3 8 5448576010_A 390 26 BXD18 P3 1 5448576045_E 392 27 BXD19 P3 8 5237939010_E 210 28 BXD19 P3 1 5448576045_A 211 29 BXD20 P3 5 5452241017_B 439 30 BXD20 P3 6 5452241033_E 441 31 BXD21 P3 7 5384138021_F 341 32 BXD21 P3 6 5384138053_F 315 33 BXD24a P3 8 5237939012_B 251 34 BXD24a P3 7 5384138020_B 250 35 BXD27 P3 8 5237939012_D 298 36 BXD27 P3 1 5448576045_C 300 37 BXD28 P3 2 5384138049_B 550 38 BXD28 P3 1 5448576029_F 548 39 BXD29 P3 2 5384138047_F 502 40 BXD29 P3 1 5448576029_D 501 41 BXD31 P3 5 5452241024_D 579 42 BXD31 P3 6 5452241035_D 582 43 BXD32 P3 5 5452241006_F 407 44 BXD32 P3 6 5452241033_C 408 45 BXD34 P3 8 5237939012_F 345 46 BXD34 P3 4 5452241022_F 355 47 BXD36 P3 7 5384138016_A 429 48 BXD36 P3 8 5448576010_D 430 49 BXD38 P3 2 5384138041_F 327 50 BXD38 P3 3 5384138058_E 328 51 BXD39 P3 7 5384138016_E 515 52 BXD39 P3 5 5452241024_A 518 53 BXD40 P3 2 5384138041_C 373 54 BXD40 P3 3 5452241008_A 375 55 BXD42 P3 3 5452241008_E 485 56 BXD42 P3 4 5452241023_F 486 57 BXD51 P3 5 5452241024_F 621 58 BXD51 P3 6 5452241035_F 622 59 BXD61 P3 4 5452241031_C 554 60 BXD61 P3 3 5452241034_A 552 61 BXD70 P3 2 5384138049_D 590 62 BXD70 P3 1 5448576044_B 589 63 BXD73 P3 2 5384138049_E 603 64 BXD73 P3 8 5448576011_E 605

About the array platform:

About data values and data processing:

Notes:

Experiment Type:

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. 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.

Contributor:

Citation:

Data source acknowledgment:

Study Id:

99

• The UT Center for Integrative and Translational Genomics
• NIGMS Systems Genetics and Precision Medicine project (R01 GM123489, 2017-2021)
• NIDA NIDA Core Center of Excellence in Transcriptomics, Systems Genetics, and the Addictome (P30 DA044223, 2017-2022)
• NIA Translational Systems Genetics of Mitochondria, Metabolism, and Aging (R01AG043930, 2013-2018)
• NIAAA Integrative Neuroscience Initiative on Alcoholism (U01 AA016662, U01 AA013499, U24 AA013513, U01 AA014425, 2006-2017)
• NIDA, NIMH, and NIAAA (P20-DA 21131, 2001-2012)
• NCI MMHCC (U01CA105417), NCRR, BIRN, (U24 RR021760)