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

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.

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: