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

single-nucleus ATAC-seq

reads

fastq

10x multiome

multiplexed sample: Homo sapiens (female, 83 years) substantia nigra tissue associated with Parkinson's disease, cerebral amyloid angiopathy, mild cognitive impairment; Homo sapiens (male, 78 years) posterior cingulate gyrus tissue associated with Parkinson's disease; ... and 10 more samples

single-nucleus ATAC-seq (10x multiome)

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

single-nucleus RNA sequencing assay

reads

fastq

10x multiome

multiplexed sample: Homo sapiens (male, 80 years) middle temporal gyrus tissue associated with Alzheimer disease, Parkinson's disease, cerebral amyloid angiopathy; Homo sapiens (male, 60 years) putamen tissue associated with Parkinson's disease; ... and 10 more samples

single-nucleus RNA sequencing assay (10x multiome)

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-nucleus ATAC-seq

reads

fastq

10x multiome

multiplexed sample: Homo sapiens (female, 82 years) substantia nigra tissue associated with cerebral amyloid angiopathy; Homo sapiens (female, 84 years) cerebellar cortex tissue associated with Parkinson's disease, mild cognitive impairment; ... and 10 more samples

single-nucleus ATAC-seq (10x multiome)

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) 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

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

single-nucleus ATAC-seq

reads

fastq

10x multiome

multiplexed sample: Homo sapiens (male, 79 years) posterior cingulate gyrus tissue; Homo sapiens (male, 80 years) posterior cingulate gyrus tissue associated with Parkinson's disease, cerebral amyloid angiopathy, mild cognitive impairment; ... and 8 more samples

single-nucleus ATAC-seq (10x multiome)

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

single-cell RNA sequencing assay

seqspec, reads

yaml, fastq

10x multiome with scMito-seq

Homo sapiens (male, 29 years) peripheral blood mononuclear cell

10x multiome with scMito-seq

single-nucleus ATAC-seq

reads

fastq

10x multiome

multiplexed sample: Homo sapiens (male, 87 years) cerebellar cortex tissue associated with Parkinson's disease, cerebral amyloid angiopathy; Homo sapiens (male, 72 years) middle temporal gyrus tissue associated with Parkinson's disease; ... and 10 more samples

single-nucleus ATAC-seq (10x multiome)

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

single-nucleus ATAC-seq

reads, seqspec

fastq, yaml

10x multiome

multiplexed sample: Homo sapiens (female, 27.0 years) peripheral blood mononuclear cell; Homo sapiens (female, 48.0 years) peripheral blood mononuclear cell; ... and 17 more samples

single-nucleus ATAC-seq (10x multiome)

single-nucleus ATAC-seq

reads

fastq

10x multiome

multiplexed sample: Homo sapiens (female, 83 years) putamen tissue associated with Parkinson's disease, cerebral amyloid angiopathy; Homo sapiens (male, 81 years) posterior cingulate gyrus tissue associated with Parkinson's disease, cerebral amyloid angiopathy; ... and 10 more samples

single-nucleus ATAC-seq (10x multiome)

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

single-nucleus ATAC-seq

reads

fastq

10x multiome

multiplexed sample: Homo sapiens (female, 78 years) putamen tissue associated with Parkinson's disease; Homo sapiens (male, 53 years) middle temporal gyrus tissue; ... and 10 more samples

single-nucleus ATAC-seq (10x multiome)

single-nucleus ATAC-seq

reads

fastq

10x multiome

multiplexed sample: Homo sapiens (male, 70 years) substantia nigra tissue associated with Parkinson's disease; Homo sapiens (male, 80 years) posterior cingulate gyrus tissue; ... and 10 more samples

single-nucleus ATAC-seq (10x multiome)

single-nucleus RNA sequencing assay

reads

fastq

10x multiome

multiplexed sample: Homo sapiens (male, 70 years) substantia nigra tissue associated with Parkinson's disease; Homo sapiens (male, 80 years) posterior cingulate gyrus tissue; ... and 10 more samples

single-nucleus RNA sequencing assay (10x multiome)

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