single-nucleus RNA sequencing assay

reads, seqspec

fastq, yaml

10x multiome with MULTI-seq

multiplexed sample: Homo sapiens (mixed sex) induced pluripotent stem differentiated cell specimen induced to islet of Langerhans for 11 days; Homo sapiens (mixed sex) induced pluripotent stem differentiated cell specimen induced to islet of Langerhans for 3 days; ... and 6 more samples

single-nucleus RNA sequencing assay (10x multiome with MULTI-seq)

in vitro CRISPR screen using flow cytometry

reads

fastq

CRISPR FACS screen

Homo sapiens (male) HepG2 cell line (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

Homo sapiens HUDEP-2 cell line 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

Homo sapiens (male) HepG2 cell line (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

single-cell ATAC-seq

reads, seqspec

fastq, yaml

SHARE-seq

Mus musculus C57BL/6 (female) brain tissue (cellular sub pool: SS-PKR 130)

single-cell ATAC-seq (SHARE-seq)

in vitro CRISPR screen using flow cytometry

reads

fastq

Variant-EFFECTS

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

Homo sapiens (female) TeloHAEC cell line (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

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

Homo sapiens (female) TeloHAEC cell line (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

Homo sapiens (male) THP-1 cell line modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) 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

Homo sapiens CD8-positive, alpha-beta memory T cell 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

Homo sapiens (male) HCT116 cell line (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

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

Homo sapiens CD8-positive, alpha-beta memory T cell (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

seqspec, reads

yaml, fastq

SHARE-seq

Mus musculus C57BL/6J colon tissue

single-cell RNA sequencing assay (SHARE-seq)

single-cell RNA sequencing assay

reads

fastq

SHARE-seq

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

single-cell RNA sequencing assay (SHARE-seq)

single-nucleus methylcytosine and transcriptome sequencing assay

reads

fastq

snMCT-seq

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

snMCT-seq

in vitro CRISPR screen using flow cytometry

seqspec, reads

yaml, fastq

CRISPR FlowFISH screen

Homo sapiens (male) HCT116 cell line (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

Homo sapiens (male) HCT116 cell line (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

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

single-nucleus RNA sequencing assay (10x multiome)

single-nucleus RNA sequencing assay

reads, seqspec

fastq, yaml

10x multiome

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

single-nucleus RNA sequencing assay (10x multiome)

bulk assay for transposase-accessible chromatin using sequencing

reads

fastq

ATAC-seq

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

ATAC-seq

single-nucleus methylcytosine and transcriptome sequencing assay

reads

fastq

snMCT-seq

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

snMCT-seq

single-nucleus RNA sequencing assay

reads, seqspec

fastq, yaml

10x multiome

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

single-nucleus RNA sequencing assay (10x multiome)

massively parallel reporter assay

reads

fastq

MPRA

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

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