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Series GSE120861 Query DataSets for GSE120861
Status Public on Jan 04, 2019
Title A genome-wide framework for mapping gene regulation via cellular genetic screens
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Over one million candidate regulatory elements have been identified across the human genome, but nearly all are unvalidated and their target genes uncertain. Approaches based on human genetics are limited in scope to common variants, and in resolution by linkage disequilibrium. We present a multiplex, eQTL-inspired framework for mapping enhancer-gene pairs by introducing random combinations of CRISPR/Cas9-mediated perturbations to each of many cells, followed by single-cell RNA-seq. Across two experiments, we used dCas9-KRAB to perturb 5,920 candidate enhancers with no strong a priori hypothesis as to their target gene(s), measuring effects by profiling 254,974 single-cell transcriptomes. We identified 664 (470 high-confidence) cis enhancer-gene pairs, which were enriched for specific transcription factors, non-housekeeping status, and genomic and 3D conformational proximity to their target genes. This framework will facilitate the large-scale mapping of enhancer-gene regulatory interactions, a critical yet largely uncharted component of the cis-regulatory landscape of the human genome.
Overall design Three scRNA-seq datasets of a low multiplicity-of-infection (MOI) pilot gRNA screen, high MOI pilot, and at-scale screen, in addition to bulkRNA-seq used to validate individual enhancer-gene pairs from the screens.
Contributor(s) Gasperini M
Citation(s) 30612741
Submission date Oct 04, 2018
Last update date Apr 04, 2019
Contact name Molly Gasperini
Organization name University of Washington
Department Genome Sciences
Street address 3720 15th Ave NE
State/province WA
ZIP/Postal code 98195
Country USA
Platforms (2)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (53)
GSM3417251 Pilot Screen (low MOI) transcriptomes scRNA-seq
GSM3417252 Pilot Screen (low MOI) gRNA enrichment scRNA-seq
GSM3417253 Pilot Screen (high MOI) transcriptomes scRNA-seq
BioProject PRJNA494734
SRA SRP163514

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SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE120861_50k_reference_cells.rds.gz 361.0 Kb (ftp)(http) RDS
GSE120861_all_deg_results.at_scale.txt.gz 35.5 Mb (ftp)(http) TXT
GSE120861_all_deg_results.pilot.txt.gz 17.9 Mb (ftp)(http) TXT
GSE120861_at_scale_screen.cds.rds.gz 1.8 Gb (ftp)(http) RDS
GSE120861_at_scale_screen.cells.txt.gz 918.7 Kb (ftp)(http) TXT
GSE120861_at_scale_screen.exprs.mtx.gz 8.9 Gb (ftp)(http) MTX
GSE120861_at_scale_screen.genes.txt.gz 42.5 Kb (ftp)(http) TXT
GSE120861_at_scale_screen.phenoData.txt.gz 82.7 Mb (ftp)(http) TXT
GSE120861_gene_gRNAgroup_pair_table.at_scale.txt.gz 18.8 Mb (ftp)(http) TXT
GSE120861_gene_gRNAgroup_pair_table.pilot.txt.gz 9.5 Mb (ftp)(http) TXT
GSE120861_grna_groups.at_scale.txt.gz 124.1 Kb (ftp)(http) TXT
GSE120861_grna_groups.pilot.txt.gz 37.6 Kb (ftp)(http) TXT
GSE120861_pilot_highmoi_screen.cds.rds.gz 422.0 Mb (ftp)(http) RDS
GSE120861_pilot_highmoi_screen.cells.txt.gz 218.3 Kb (ftp)(http) TXT
GSE120861_pilot_highmoi_screen.exprs.mtx.gz 2.2 Gb (ftp)(http) MTX
GSE120861_pilot_highmoi_screen.genes.txt.gz 104.0 Kb (ftp)(http) TXT
GSE120861_pilot_highmoi_screen.phenoData.txt.gz 16.3 Mb (ftp)(http) TXT
GSE120861_pilot_lowmoi_screen.cds.rds.gz 346.7 Mb (ftp)(http) RDS
GSE120861_pilot_lowmoi_screen.cells.txt.gz 191.0 Kb (ftp)(http) TXT
GSE120861_pilot_lowmoi_screen.exprs.mtx.gz 1.9 Gb (ftp)(http) MTX
GSE120861_pilot_lowmoi_screen.genes.txt.gz 104.0 Kb (ftp)(http) TXT
GSE120861_pilot_lowmoi_screen.phenoData.txt.gz 4.1 Mb (ftp)(http) TXT
GSE120861_sequence_deletions_normalized_tpms.tsv.gz 18.3 Mb (ftp)(http) TSV
GSE120861_singletons_set1_normalized_tpms.tsv.gz 11.9 Mb (ftp)(http) TSV
GSE120861_singletons_set2_normalized_tpms.tsv.gz 38.4 Mb (ftp)(http) TSV
GSE120861_zero_inflated_outlier_genes_to_exclude.atscale.txt.gz 838 b (ftp)(http) TXT
GSE120861_zero_inflated_outlier_genes_to_exclude.pilot.txt.gz 943 b (ftp)(http) TXT
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