Pluto Bioinformatics

GSE145485: RNA-Sequencing of LPS-stimulated TLR4 HEK293 cells with CRISPRi treatment at an immune enhancer

Bulk RNA sequencing

In order to investigate the role of an IRF1-associated trans-response eQTL in immune response, we utilized CRISPRi to repress either the eQTL variant locus or the promoter of IRF1. Cells were treated with a CRISPRi construct and gRNAs targeting a putative IRF1 enhancer, the IRF1 promoter or GFP (control). RNA-sequencing was performed with no stimulation, with 90min LPS stimulation and 12h LPS stimulation, with two replicates of each for each gRNA condition. We find a correlation in the fold changes of differentially expressed genes in the promoter and enhancer gRNA conditions, suggesting the enhancer is indeed affecting expression of IRF1 and producing a similar effect on the transcriptome. SOURCE: Margot Brandt (mbrandt@nygenome.org) - Lappalainen Lab New York Genome Center