Mice were purchased at 7-8 weeks of age from Charles River laboratory
Extracted molecule
total RNA
Extraction protocol
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
Label
cy3
Label protocol
Standard Illumina protocol
Hybridization protocol
Standard Illumina hybridization protocol
Scan protocol
Standard Illumina scanning protocol
Description
8324341073_C
Data processing
The raw probe intensities were background subtracted and quartile normalized to adjust for variation that arose from microarray technology and not from biological differences. The normalized probe signals were then summarized into gene-level, during which signals of multiple probes that represent the same gene will be averaged to obtain gene expression level in GenomeStudio™ and exported as a tab-delimited txt file, which was imported into Partek, minimum value shifted to 1.0, and log2 transformed [*gene_level.txt]. Genes that were not expressed in any sample (Non-expressed genes, NEGs, identified by detection P value >= 0.05) were removed from further studies removed to improve the sensitivity of differential gene expression detection If a gene is expressed in at least one of the 12 samples, the gene was kept for final output; if a gene is not expressed in any sample, it was excluded from subsequent analysis. After this pre-filtering step, 16,410 out of 30,854 genes (53.2%) were kept for DEG detection in Partek.
