10x multiome with MULTI-seq

GRCh38

index, cell hashing barcodes, fragments, peaks, raw feature barcode matrix

tbi, tsv, bed, hdf5

intermediate analysis

multiplexed sample: Homo sapiens (female) H7-hESC differentiated cell specimen; Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 6 days; ... and 10 more samples

10x multiome with MULTI-seq: cell hashing barcodes, fragments, index, peaks, raw feature barcode matrix

intermediate analysis

Unspecified assay

lentiMPRA

hg19

reporter genomic variant effects

tsv

principal analysis

Homo sapiens (male) H1-hESC pooled differentiated cell specimen induced to glutamatergic neuron for 7 days transduced (lentivirus) with a reporter library

lentiMPRA: reporter genomic variant effects

HiCAR

contact matrix

mcool, cool

intermediate analysis

Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 42 days treated with 1 μM Endothelin-1 for 3 days, transfected with a guide library

HiCAR: contact matrix

ATAC-seq

GRCh38

fold change over control, peak quantifications, alignments

tsv, bam

principal analysis

Homo sapiens CD8-positive, alpha-beta memory T cell transduced (lentivirus) with a expression vector library

ATAC-seq: alignments, fold change over control, peak quantifications

Perturb-seq

sparse gene count matrix, filtered feature barcode matrix, raw feature barcode matrix

h5ad, hdf5, pkl

principal analysis

Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW262) modified with CRISPRi Sp-dCas9, 3 week(s) after transfection with a guide library, Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW268) modified with CRISPRi Sp-dCas9, 3 week(s) after transfection with a guide library, Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW265) modified with CRISPRi Sp-dCas9, 3 week(s) after transfection with a guide library, Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW263) modified with CRISPRi Sp-dCas9, 3 week(s) after transfection with a guide library, Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW261) modified with CRISPRi Sp-dCas9, 3 week(s) after transfection with a guide library, Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW267) modified with CRISPRi Sp-dCas9, 3 week(s) after transfection with a guide library, Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW264) modified with CRISPRi Sp-dCas9, 3 week(s) after transfection with a guide library, Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW266) modified with CRISPRi Sp-dCas9, 3 week(s) after transfection with a guide library

interference Perturb-seq: filtered feature barcode matrix, raw feature barcode matrix, sparse gene count matrix

Perturb-seq

sparse gene count matrix, filtered feature barcode matrix, raw feature barcode matrix, unfiltered local differential expression, unfiltered global differential expression

h5ad, hdf5, pkl, csv

principal analysis

Homo sapiens (female) H9 differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW423) modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library, Homo sapiens (female) H9 differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW422) modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library, Homo sapiens (female) H9 differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW421) modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library, Homo sapiens (female) H9 differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW424) modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library

interference Perturb-seq: filtered feature barcode matrix, raw feature barcode matrix, sparse gene count matrix, unfiltered global differential expression, unfiltered local differential expression

Proliferation CRISPR screen

guide quantifications

csv

principal analysis

Homo sapiens (female) TeloHAEC cell line modified with CRISPRi Sp-dCas9-KOX1-KRAB, transduced (lentivirus) with a guide library

Proliferation CRISPR interference screen: guide quantifications

10x multiome with MULTI-seq

GRCh38

peaks, index, raw feature barcode matrix, fragments, cell hashing barcodes

bed, tbi, hdf5, tsv

intermediate analysis

multiplexed sample: Homo sapiens (female) H9 differentiated cell specimen induced to neuron for 6 days; Homo sapiens (female) H9 differentiated cell specimen induced to neuron for 6 days; ... and 6 more samples

10x multiome with MULTI-seq: cell hashing barcodes, fragments, index, peaks, raw feature barcode matrix

CRISPR FACS screen

custom

guide quantifications, fold change over control, alignments

csv, tsv, bam

principal analysis

Homo sapiens CD8-positive, alpha-beta memory T cell (sorting details: FACS bin for 90-100% expression of CCR7) modified with CRISPRa Sa-dCas9-VP64, transduced (lentivirus) with a guide library (MOI of 0.4), Homo sapiens CD8-positive, alpha-beta memory T cell (sorting details: FACS bin for 0-10% expression of CCR7) modified with CRISPRa Sa-dCas9-VP64, transduced (lentivirus) with a guide library (MOI of 0.4)

CRISPR activation FACS screen targeting CCR7: alignments, fold change over control, guide quantifications

10x multiome with MULTI-seq

GRCh38

fragments, raw feature barcode matrix, cell hashing barcodes, peaks, index

tsv, hdf5, bed, tbi

intermediate analysis

multiplexed sample: Homo sapiens (male) H1-hESC differentiated cell specimen induced to islet of Langerhans for 18 days; Homo sapiens (male) H1-hESC differentiated cell specimen induced to islet of Langerhans for 7 days; ... and 6 more samples

10x multiome with MULTI-seq: cell hashing barcodes, fragments, index, peaks, raw feature barcode matrix

HiCAR

contact matrix

mcool, cool

intermediate analysis

Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 42 days treated with 1 μM Endothelin-1 for 3 days, transfected with a guide library

HiCAR: contact matrix

HiCAR

contact matrix

mcool, cool

intermediate analysis

Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 42 days transfected with a guide library

HiCAR: contact matrix

10x multiome with MULTI-seq

GRCh38

cell hashing barcodes, fragments, index, peaks, raw feature barcode matrix

tsv, tbi, bed, hdf5

intermediate analysis

multiplexed sample: Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to liver for 18 days; Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to liver for 13 days; ... and 10 more samples

10x multiome with MULTI-seq: cell hashing barcodes, fragments, index, peaks, raw feature barcode matrix

10x multiome with MULTI-seq

GRCh38

peaks, index, fragments, cell hashing barcodes, raw feature barcode matrix

bed, tbi, tsv, hdf5

intermediate analysis

multiplexed sample: Homo sapiens (female) H9 differentiated cell specimen induced to cardiac muscle cell for 15 days; Homo sapiens (male) HepG2 cell line grown in DMEM without serum; ... and 10 more samples

10x multiome with MULTI-seq: cell hashing barcodes, fragments, index, peaks, raw feature barcode matrix

HiCAR

contact matrix

mcool, cool

intermediate analysis

Mus musculus C57BL/6J (female) HL-1 cell line transfected with a guide library

HiCAR: contact matrix

SHARE-seq

sparse gene count matrix, fragments

h5ad, tsv

intermediate analysis

Mus musculus C57BL/6J colon tissue

SHARE-seq: fragments, sparse gene count matrix

intermediate analysis

Unspecified assay

10x multiome with MULTI-seq

GRCh38

peaks, fragments, index, raw feature barcode matrix, cell hashing barcodes

bed, tsv, tbi, hdf5

intermediate analysis

multiplexed sample: Homo sapiens (female) B differentiated cell specimen induced to plasmablast for 6 days; Homo sapiens (female) B differentiated cell specimen induced to plasmablast for 5 days; ... and 10 more samples

10x multiome with MULTI-seq: cell hashing barcodes, fragments, index, peaks, raw feature barcode matrix

Variant-EFFECTS

hg19, GRCh38

variant effects

tsv

principal analysis

Homo sapiens (male) THP-1 cell line (sorting details: FACS bin for 0-10% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library, Homo sapiens (male) THP-1 cell line (sorting details: FACS bin for 80-90% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library, Homo sapiens (male) THP-1 cell line (sorting details: FACS bin for 35-45% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library, Homo sapiens (male) THP-1 cell line modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library, Homo sapiens (male) THP-1 cell line (sorting details: FACS bin for 55-65% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library, Homo sapiens (male) THP-1 cell line (sorting details: FACS bin for 90-100% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library, Homo sapiens (male) THP-1 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, Homo sapiens (male) THP-1 cell line modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2)

prime editing Variant-EFFECTS targeting PPIF: variant effects

ATAC-seq

GRCh38

fold change over control, peak quantifications, alignments

tsv, bam

principal analysis

Homo sapiens CD8-positive, alpha-beta memory T cell transduced (lentivirus) with a expression vector library

ATAC-seq: alignments, fold change over control, peak quantifications

HiCAR

contact matrix

mcool, cool

intermediate analysis

Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 42 days transfected with a guide library

HiCAR: contact matrix

Perturb-seq

sparse gene count matrix, filtered feature barcode matrix, raw feature barcode matrix, unfiltered local differential expression, unfiltered global differential expression

h5ad, hdf5, pkl, csv

principal analysis

Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW267) modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library, Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW262) modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library, Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW261) modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library, Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW266) modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library, Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW263) modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library, Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW264) modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library, Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW268) modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library, Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW265) modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library

interference Perturb-seq: filtered feature barcode matrix, raw feature barcode matrix, sparse gene count matrix, unfiltered global differential expression, unfiltered local differential expression

RNA-seq

GRCh38

transcript quantifications, fold change over control, transcriptome alignments

tsv, csv, bam

principal analysis

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, Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 28 days

RNA-seq: fold change over control, transcript quantifications, transcriptome alignments

intermediate analysis

Unspecified assay