in vitro CRISPR screen using flow cytometry

reads

fastq

CRISPR FACS screen

HepG2 cell line, male, Homo sapiens (sorting details: Sorted for Bottom 20% LDL-C uptake) modified with CRISPR base editing SpRY-ABE8e, transduced (lentivirus) with a guide library (MOI of 0.5)

CRISPR base editing FACS screen integrating a guide (sgRNA) library targeting phenotype-associated variants genome-wide

in vitro CRISPR screen assay

reads

fastq

Proliferation CRISPR screen

HUDEP-2 cell line, Homo sapiens modified with CRISPR cutting SpRY, transduced (lentivirus) with a guide library

Proliferation CRISPR cutting screen integrating a guide (sgRNA) library targeting phenotype-associated variants genome-wide

in vitro CRISPR screen using flow cytometry

reads

fastq

CRISPR FACS screen

HepG2 cell line, male, Homo sapiens (sorting details: Sorted for Top 20% LDL-C uptake) modified with CRISPR base editing SpRY-ABE8e, transduced (lentivirus) with a guide library (MOI of 0.5)

CRISPR base editing FACS screen integrating a guide (sgRNA) library targeting phenotype-associated variants genome-wide

in vitro CRISPR screen using flow cytometry

reads

fastq

Variant-EFFECTS

THP-1 cell line, male, Homo sapiens (sorting details: FACS bin for 0-25% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transfected with a guide library

CRISPR prime editing Variant-EFFECTS sorted on the expression of PPIF integrating a guide (sgRNA) library targeting sequence variants in a genomic locus

in vitro CRISPR screen using flow cytometry

reads

fastq

Variant-EFFECTS

Jurkat cell line, male, Homo sapiens (sorting details: FACS bin for 11-20% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transfected with a guide library

CRISPR prime editing Variant-EFFECTS sorted on the expression of PPIF integrating a guide (sgRNA) library targeting sequence variants in a genomic locus

in vitro CRISPR screen using flow cytometry

reads

fastq

CRISPR FlowFISH screen

TeloHAEC cell line, female, Homo sapiens (sorting details: FACS 60-80% expression of NFKBIA) modified with CRISPRi Sp-dCas9-KOX1-KRAB, transduced (lentivirus) with a guide library

CRISPR interference FlowFISH screen sorted on the expression of NFKBIA integrating a guide (sgRNA) library targeting phenotype-associated variants genome-wide associated with blood pressure

in vitro CRISPR screen using flow cytometry

reads

fastq

Variant-EFFECTS

THP-1 cell line, male, Homo sapiens (sorting details: FACS bin for 0-25% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transfected with a guide library

CRISPR prime editing Variant-EFFECTS sorted on the expression of PPIF integrating a guide (sgRNA) library targeting sequence variants in a genomic locus

in vitro CRISPR screen using flow cytometry

reads

fastq

CRISPR FlowFISH screen

TeloHAEC cell line, female, Homo sapiens (sorting details: FACS bin for 76-100% expression of TLNRD1) modified with CRISPRi Sp-dCas9-KOX1-KRAB, transfected with a guide library

CRISPR interference FlowFISH screen sorted on the expression of TLNRD1 integrating a guide (sgRNA) library targeting candidate cis-regulatory elements in a genomic locus

in vitro CRISPR screen using flow cytometry

reads

fastq

Variant-EFFECTS

THP-1 cell line, male, Homo sapiens modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transfected with a guide library

unsorted FACS input CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus

bulk RNA-seq assay

reads

fastq

RNA-seq

CD8-positive, alpha-beta memory T cell, Homo sapiens modified with CRISPRko Sp-Cas9, transduced (lentivirus) with a guide library (MOI of 0.4)

CRISPR knockout RNA-seq integrating a guide (sgRNA) library targeting transcription start sites in GATA3

in vitro CRISPR screen using flow cytometry

seqspec, reads

yaml, fastq

CRISPR FlowFISH screen

HCT116 cell line, male, Homo sapiens (sorting details: FACS bin F for 80-100% expression of KITLG) modified with CRISPRi Sp-dCas9-KOX1-KRAB, inactive AID system targeting RAD21, transfected with a guide library

mixed CRISPR FlowFISH screen sorted on the expression of KITLG integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci

in vitro CRISPR screen using flow cytometry

reads

fastq

Variant-EFFECTS

THP-1 cell line, male, Homo sapiens (sorting details: FACS bin for 26-50% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transfected with a guide library

CRISPR prime editing Variant-EFFECTS sorted on the expression of PPIF integrating a guide (sgRNA) library targeting sequence variants in a genomic locus

in vitro CRISPR screen using flow cytometry

reads

fastq

CRISPR FACS screen

CD8-positive, alpha-beta memory T cell, Homo sapiens (sorting details: FACS bin for 90-100% expression of IL7R in cells overexpressing BATF3) modified with CRISPRko Sp-Cas9, transduced (lentivirus) with multiple libraries (MOI of 0.4)

CRISPR knockout FACS screen sorted on the expression of IL7R integrating a guide (sgRNA) library targeting transcription start sites in many genes and an expression vector library of BATF3

single-cell RNA sequencing assay

reads

fastq

SHARE-seq

colon tissue, Mus musculus C57BL/6J

single-cell RNA sequencing assay (SHARE-seq)

single-cell RNA sequencing assay

reads

fastq

SHARE-seq

bone marrow cell (cellular sub pool: SS-PKR 1), male, Homo sapiens (37 years)

single-cell RNA sequencing assay (SHARE-seq)

single-nucleus methylcytosine and transcriptome sequencing assay

reads

fastq

snMCT-seq

fibroblast reprogrammed cell specimen induced to induced pluripotent stem cell for 3 days, Homo sapiens

snMCT-seq

in vitro CRISPR screen using flow cytometry

seqspec, reads

yaml, fastq

CRISPR FlowFISH screen

HCT116 cell line, male, Homo sapiens (sorting details: FACS bin C for 35-45% expression of KITLG) treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours, modified with AID system targeting RAD21, CRISPRi Sp-dCas9-KOX1-KRAB, transfected with a guide library

mixed CRISPR FlowFISH screen sorted on the expression of KITLG integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci

in vitro CRISPR screen using flow cytometry

seqspec, reads

yaml, fastq

CRISPR FlowFISH screen

HCT116 cell line, male, Homo sapiens (sorting details: FACS bin B for 10-20% expression of KITLG) modified with CRISPRi Sp-dCas9-KOX1-KRAB, inactive AID system targeting RAD21, transfected with a guide library

mixed CRISPR FlowFISH screen sorted on the expression of KITLG integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci

single-nucleus RNA sequencing assay

reads, seqspec

fastq, yaml

10x multiome

left cerebral cortex tissue, male, Mus musculus C57BL/6J (10 weeks)

single-nucleus RNA sequencing assay (10x multiome)

single-nucleus RNA sequencing assay

reads, seqspec

fastq, yaml

10x multiome

left cerebral cortex tissue, male, Mus musculus C57BL/6J (10 weeks)

single-nucleus RNA sequencing assay (10x multiome)

bulk assay for transposase-accessible chromatin using sequencing

reads

fastq

ATAC-seq

GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 28 days, male, Homo sapiens treated with 4 μM GSK3 inhibition for 7 days

ATAC-seq

single-nucleus methylcytosine and transcriptome sequencing assay

reads

fastq

snMCT-seq

fibroblast reprogrammed cell specimen induced to induced pluripotent stem cell for 1 day, Homo sapiens

snMCT-seq

massively parallel reporter assay

reads

fastq

MPRA

mouse embryonic stem differentiated cell specimen induced to embryoid body for 14 days, male, Mus musculus WD44 transfected with a reporter library

MPRA integrating a reporter library targeting accessible genome regions in many genomic loci

in vitro CRISPR screen using flow cytometry

reads

fastq

Variant-EFFECTS

THP-1 cell line, male, Homo sapiens (sorting details: FACS bin for 90-100% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transfected with a guide library

CRISPR prime editing Variant-EFFECTS sorted on the expression of PPIF integrating a guide (sgRNA) library targeting sequence variants in a genomic locus

in vitro CRISPR screen using flow cytometry

reads

fastq

Variant-EFFECTS

THP-1 cell line, male, Homo sapiens (sorting details: FACS bin for 76-100% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transfected with a guide library

CRISPR prime editing Variant-EFFECTS sorted on the expression of PPIF integrating a guide (sgRNA) library targeting sequence variants in a genomic locus