CRISPRi Screening of Enhancers in Human Primary Astrocytes Identifies Regulatory Circuitry Disrupted in Alzheimer’s Disease [RNA-seq]

We used CROP-seq to perform a high-throughput, parallel screen of 979 candidate enhancer perturbations in normal human astrocytes (NHAs), a primary cell-line. We identified the target gene(s) for 145 of these candidates, which were enriched for transcription with eRNA, transcription factor footprinting, and superenhancer annotation. Most regulatory interactions were <50kb, targeting the nearest gene in ~50% of cases, but were not typically captured by eQTL or in silico predictions. These data elucidate the regulatory network of an understudied-but-crucial brain cell-type. To investigate basal gene and eRNA expression, RNA sequencing was performed on Normal Human Astrocytes (NHA; Lonza) stably expressing dCas9-KRAB-Blast Three distinct libraries were prepared; mRNA-seq (to compare to scRNA-seq), ribo-depleted RNA-seq (to compare to TT-seq), and ribo-depleted RNA-seq of transient transcriptome sequencing (TT-seq) samples. Please note that the 'TTseq_RiboDep.csv' contains processed data for both 'ribo-depleted RNA-seq' and 'TT-seq' samples, and is linked to the 'ribo-depleted RNA-seq' sample records.