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

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

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 0-10% 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 90-100% 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

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

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, 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

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

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 (male) B differentiated cell specimen induced to plasmablast for 1 day; Homo sapiens (male) B differentiated cell specimen induced to plasmablast for 5 days; ... and 5 more samples

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

Proliferation CRISPR screen

guide quantifications, variant effects

csv

principal analysis

Homo sapiens HUDEP-2 cell line modified with CRISPR cutting SpRY, transduced (lentivirus) with a guide library, Homo sapiens HUDEP-2 cell line modified with CRISPR base editing SpRY-ABE8e, transduced (lentivirus) with a guide library

Proliferation CRISPR base editing, cutting screen: guide quantifications, variant effects

10x multiome with MULTI-seq

GRCh38

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

tsv, tbi, bed, hdf5

intermediate analysis

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

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 (male) Jurkat cell line (sorting details: FACS bin for 90-100% expression of IL2RA ) modified with CRISPRa Sa-dCas9-2xVP64, transduced (lentivirus) with a guide library (MOI of 0.4), Homo sapiens (male) Jurkat cell line (sorting details: FACS bin for 0-10% expression of IL2RA ) modified with CRISPRa Sa-dCas9-2xVP64, transduced (lentivirus) with a guide library (MOI of 0.4)

CRISPR activation FACS screen targeting IL2RA: alignments, fold change over control, guide quantifications

CRISPR FlowFISH screen

guide quantifications

csv

principal analysis

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, Homo sapiens (female) TeloHAEC cell line (sorting details: FACS 0-20% expression of NFKBIA) modified with CRISPRi Sp-dCas9-KOX1-KRAB, transduced (lentivirus) with a guide library, Homo sapiens (female) TeloHAEC cell line (sorting details: FACS 20-40% expression of NFKBIA) modified with CRISPRi Sp-dCas9-KOX1-KRAB, transduced (lentivirus) with a guide library, Homo sapiens (female) TeloHAEC cell line (sorting details: FACS 80-100% expression of NFKBIA) modified with CRISPRi Sp-dCas9-KOX1-KRAB, transduced (lentivirus) with a guide library

CRISPR interference FlowFISH screen targeting NFKBIA: guide quantifications

CRISPR FACS screen

variant effects, guide quantifications

csv

principal analysis

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), Homo sapiens (male) HepG2 cell line modified with CRISPR base editing SpRY-ABE8e, transduced (lentivirus) with a guide library (MOI of 0.5), 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), Homo sapiens (male) HepG2 cell line (sorting details: Sorted for Bottom 20-40% LDL-C uptake) modified with CRISPR base editing SpRY-ABE8e, transduced (lentivirus) with a guide library (MOI of 0.5), Homo sapiens (male) HepG2 cell line (sorting details: Sorted for Top 20-40% 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: guide quantifications, variant effects