GSE110422
Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and NCoR1 KD  CD8a+ Dendritic cells with and without CpG stimulation
Purpose: The goals of this study to dissect mechanism by which NCoR1 regulate expression of diiferent genes at transcriptional level in CD8a+ Dendritic cells. Methods: mRNA expression of  Control(Empty) and knockdown (NCoR1+/-) before and after CpG and pIC activation were generated by deep sequencing, in duplicate, using Illumina NextSeq 500 . The sequence reads that passed quality filters were analyzed at the transcript level with two methods:TopHat followed by Cufflinks. Results: we mapped raw reads to the mouse genome (build mm10) with TopHat. Differential expression study was carried out using Cufflinks v2.2.1 and list were filtered using fold change cut-off of 2 and q value <0.05. Conclusions: We found in our study that NCoR1 knock down dendritic cells (DCs) develop tolerogenic behavior upon activation and these cells have the potential to modulate T helper cell differentiation toward Treg phenotype. Here to understand the mechanism of this process we performed NCoR1 ChIP-seq in wild type DCs before and after CpG ligand activation and transcriptome analysis of NCoR1 KD DCs to identify the direct and indirect target genes. We also predicted PU.1 as the recruting factor for NCoR1 in DCs based on motif enrichment and later on validated that by performing PU.1 ChIP-seq in control and NCoR1 KD DCs. Overall design: Mechanistic role of NCoR1 co-repressor in dendritic cell function