Genome-scale mapping of variant, enhancer and gene function in primary human CD4+ T cells

Single cell RNA-seq from naive CD4+ T cells isolated from blood from three healthy female donors, stimulated with anti-CD3/CD28 beads, infected with lentiviral dCas9-ZIM3-KRAB and a gRNA library and then reactivated. CRE screen: 1,032 putative CREs are perturbed with CRISPRi and the expression of specifically targeted gene sets is read out (TAP-seq). panel*_seurat.rds: Seurat files per TAP-seq panel, 3 donors combined. panel*_seurat_grna_annotated.rds: Seurat files per TAP-seq panel, 3 donors combined, cells filtered for having 1 gRNA assigned. Promoter screen: 7,664 promoters are perturbed with CRISPRi (Perturb-seq). Perturbation information in gRNA libraries, whole transcriptome in WTX libraries. promoter_single_guide_hvg_raw_counts_uint16.h5ad: AnnData object with per cell raw counts. Annotations: bpcells_name: Unique cell identifier batch: Library (donor + chip) guide: CRISPR guide RNA (gRNA) assigned to each cell guide_idx: Numeric index encoding the guide RNA identity target_idx: Numeric index encoding the target gene perturbed by the guide RNA target: Gene targeted by the CRISPR guide RNA donor: Biological donor of origin for each cell Alignment: BD Rhapsody v2.2 pipeline Filtering: >1000 genes, <15% ribosomal reads, <10% mitochondrial reads gRNA assignment: SCEPTRE v0.10.3 Filtering: cells with 1 gRNA assigned Filtering: gene expression for 8,001 variable genes