title: rs6446275_homo_3-3b_S5
design: Total RNA was extracted using the RNeasy Micro Kit. The total RNA quality was assessed via an Agilent RNA 6000 Pico Kit. Two nanogram of total RNA was used for cDNA synthesis and 125pg of cDNA for the RNA-sequencing library preparation using the Nextera XT DNA Library Prep Kit. Briefly, we generated 50-37 bp Paired End Sequencing at the University of Chicago Genomics Core facility. We then aligned the data using STAR (v2.7.10a). Gene level counts were produced using the built in htseq-count utility in STAR. We then analyzed the counts data in R using the edgeR library for differential expression analyses on counts data. We employed pre-filtering and TMM normalization, followed by modeling allelic deletion effect sizes using the quasi-likelihood generalized linear model approach. We controlled type-I error using FDR corrections and a 5% threshold on q-values. Experimental batch variables were included in models to account for global differences in gene expression arising from differences in experimental preparation and cell culture.