Data Set Group2: BIDMC/UTHSC Dev Striatum P3 ILMv6.2 (Nov10)

Data Set: BIDMC/UTHSC Dev Striatum P3 ILMv6.2 (Nov11) RankInv GN Accession: GN376 GEO Series: No Geo series yet Title: Organism: Mouse (Mus musculus, mm10) Group: BXD Tissue: Striatum 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

Specifics of this Data Set:

None

Summary:

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. 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). 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). Users of these mouse striatum data set may also find the following complementary resources and papers useful: A movie of the dissection of the brain by Dr. Glenn Rosen. www.rosenlab.net/Movie/P3.mov www.rosenlab.net/Movie/P14.mov

About the cases 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. Care was taken to assure that samples were comprised of the dorsal striatum, although it is possible that ventral striatum (accumbens) was occasionally included. 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.   Index Strain Age Batch ID Sample ID Tube ID 1 BXD1 P3 8 5237939012_A 232 2 BXD1 P3 1 5448576016_C 234 3 BXD2 P3 7 5384138020_C 230 4 BXD2 P3 6 5384138053_A 228 5 BXD5 P3 6 5384138053_D 270 6 BXD5 P3 5 5452241004_E 268 7 BXD6 P3 2 5384138018_A 102 8 BXD6 P3 1 5448576016_A 101 9 BXD8 P3 3 5384138048_B 110 10 BXD9 P3 2 5384138041_A 280 11 BXD9 P3 3 5384138058_C 278 12 BXD11 P3 2 5384138018_B 121 13 BXD11 P3 3 5384138048_C 123 14 BXD12 P3 5 5452241004_A 127 15 BXD12 P3 4 5452241007_B 125 16 BXD13 P3 8 5237939010_D 181 17 BXD13 P3 1 5448576016_B 183 18 BXD14 P3 5 5452241017_A 420 19 BXD14 P3 4 5452241023_C 419 20 BXD15 P3 7 5384138016_C 475 21 BXD15 P3 8 5448576010_F 476 22 BXD16 P3 6 5384138009_F 204 23 BXD16 P3 7 5384138020_D 205 24 BXD18 P3 7 5384138017_B 388 25 BXD18 P3 3 5452241008_B 385 26 BXD19 P3 2 5384138018_E 212 27 BXD19 P3 3 5384138048_F 213 28 BXD20 P3 2 5384138047_C 431 29 BXD20 P3 1 5448576029_A 431 30 BXD21 P3 5 5452241006_A 311 31 BXD21 P3 4 5452241022_E 309 32 BXD24a P3 6 5384138053_B 247 33 BXD24a P3 4 5452241022_B 244 34 BXD27 P3 7 5384138021_D 294 35 BXD27 P3 6 5384138053_E 293 36 BXD28 P3 7 5384138016_F 543 37 BXD28 P3 8 5448576011_B 545 38 BXD29 P3 7 5384138016_D 495 39 BXD29 P3 8 5448576011_A 498 40 BXD31 P3 4 5452241031_D 577 41 BXD31 P3 3 5452241034_D 575 42 BXD32 P3 5 5452241006_E 402 43 BXD32 P3 4 5452241023_B 401 44 BXD34 P3 2 5384138041_D 348 45 BXD34 P3 1 5448576016_E 347 46 BXD36 P3 2 5384138047_B 417 47 BXD36 P3 3 5452241008_D 418 48 BXD38 P3 8 5237939012_E 321 49 BXD38 P3 1 5448576016_D 322 50 BXD39 P3 5 5452241017_F 511 51 BXD39 P3 4 5452241031_A 512 52 BXD40 P3 8 5448576010_B 368 53 BXD40 P3 1 5448576016_F 371 54 BXD42 P3 2 5384138047_E 481 55 BXD42 P3 1 5448576029_C 479 56 BXD51 P3 4 5452241031_F 616 57 BXD51 P3 3 5452241034_F 615 58 BXD61 P3 5 5452241024_C 555 59 BXD61 P3 6 5452241035_B 557 60 BXD70 P3 7 5384138017_E 584 61 BXD70 P3 8 5448576011_D 585 62 BXD73 P3 5 5452241024_E 600 63 BXD73 P3 6 5452241035_E 601

About the array platform:

About data values and data 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.

Notes:

Experiment Type:

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:

100

• 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)