Pluto Bioinformatics

GSE145486: RNA-Sequencing of LPS-stimulated TLR4 HEK293 cells edited at an immune-response trans-eQTL locus

Bulk RNA sequencing

In order to investigate the genetic effect of an IRF1-associated immune-response trans-eQTL, we used CRISPR editing to introduce deletions at the top variant rs17622517. Five unedited, three heterozygous and five homozygous clones were isolated and RNA-sequencing was performed with no stimulation, with 90min LPS stimulation and 12h LPS stimulation, with two replicates of each. We find a significant correlation between the genetic perturbation here and CRISPRi perturbation of the variant locus, as well as the trans-eQTL effects, suggesting this variant is the causal variant for the immune-response trans-eQTL. SOURCE: Margot Brandt (mbrandt@nygenome.org) - Lappalainen Lab New York Genome Center