title: RNA-seq of Th0
design: Nave CD4+ T cells were cultured under Th0 or iTreg polarization conditions and treated with OGG1 inhibitor TH5487 for 3 days. Total RNA was isolated with TRIzol (Invitrogen) and subjected to RNA-sequencing using Illumina Nextseq500 (75 bp paired end reads) by BGI Genomics Co.,Ltd. The raw reads were aligned to the mouse reference genome (version mm10), using Tophat2 RNASeq alignment software. The mapping rate was 96% overall across all the samples in the dataset. HTSeq was used to quantify the gene expression counts from Tophat2 alignment files. Differential expression analysis was performed on the count data using R package DESeq2. P-values obtained from multiple tests were adjusted using Benjamini-Hochberg correction. Significant differentially expressed genes are defined by a Benjamini-Hochberg corrected p-value cutoff of 0.05 and fold-change of at least 1.5.
library_name: Th0D3A3
identifiers.namespace: SUB15306724
identifiers.id: Th0D3A3