Total RNA was isolated from tissue (AllPrep) as suggested by the manufacturer.RNA quality was assessed on an Agilent 2100 Bioanalyzer, RNA 6000 Pico Series II Chips (Agilent, Palo Alto, CA, USA). Samples with a RIN score 2.0 or greater were passed, and quantity was determined by Nanodrop ND-1000 (Nanodrop Technologies, Wilmington, DE).
Label
biotin
Label protocol
Standard Affymetrix protocol
Hybridization protocol
Standard Affymetrix protocol
Scan protocol
Standard Affymetrix protocol
Description
wt_6m_2 LTMC083110_03_426.CEL
Data processing
Raw Data were processed with the FARMS algorithm in R/Bioconductor. probe group file: MoEx-1_0-st-v1.r2.pgf meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm9.core.mps Data filtering details: The microarray data for the paper was used primarily to analyze gene sets that were preferentially altered among differentially expressed genes. For this analysis, we restricted our set to those probes that matched genes with an Entrez Gene ID, and we required each Entrez ID in our list to be unique. Therefore, the processed data in this worksheet represents all probes with unique Entrez Gene IDs. The GPL6246 platform has 35,557 ID_REFs, out of which 6614 are control probes. Of the remaining probes that are designed to match genes, 23,858 correspond to genes with an Entrez gene ID, according to the MoGene annotation files. Of those, 22,679 represent unique Entrez gene IDs. Of those, many previous Entrez gene IDs have been removed or merged during more recent releases of the Entrez gene info database. Correspondingly, we have also removed the entries for which the Entrez_gene_ID has been removed or merged with another gene. This left 20,670 entries with a unique and current Entrez gene ID which represents the dataset used for this paper.
