mouse interferon gamma, 10 ng/ml final concentration
Growth protocol
DMEM, 10% FCS, pen+strep
Extracted molecule
total RNA
Extraction protocol
Trizol
Label
Cy3
Label protocol
Cy3
Hybridization protocol
Agilent's SurePrint G3 Mouse GE 8x60K Microarray, (Agilent Microarray Design ID 028005).RNA quality was checked on RNA 6000 Nano chips using a Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA, USA). Agilent’s Low Input Quick Amp Labeling Kit, one-color was used to generate fluorescent cRNA. The amplified cyanine 3-labeled cRNA samples were then purified using Promega’s SV Total RNA Isolation System and hybridized to Agilent Whole Mouse Genome Microarrays, 8x60K.
Scan protocol
Agilent Scanner, according to the standard protocol of the manufacturer
Description
SAMPLE 5
Data processing
Further analyses were performed using Bioconductor rooted in the statistical computing environment R. The raw intensities were imported into Bioconductor and further processed with the limma package. Quality Controls were performed using the arrayQualityMetrics package. The outlier array #10 [SA.CDK.gamma.R3] was removed from subsequent analysis. Normalization between arrays was performed using the quantile method, duplicate probes were averaged and a linear model also including a batch effect between Biological Replicates 1 and 2&3 was fitted due to a batch effect shown by the QA PCA plots. P-values were adjusted for multiple testing using the Benjamini & Hochberg method.