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IGVFDS2018URDY

released
Aliases
ansuman-satpathy:igvf10_analysis_set
File Set Type
intermediate analysis
Summary
10x multiome with MULTI-seq: cell hashing barcodes, fragments, index, peaks, raw feature barcode matrix
Description
Quality-control workflow performed by Satpathy Lab - K562-CRISPRi, THP1, Jurkat, Jurkat + CD3/PMA, TeloHAEC-CRISPRi
Workflows
Samples
K562, THP-1, Jurkat, TeloHAEC cell line and multiplexed sample, stimulated with treatment(s), modified with CRISPR modifications
Protocols

Files

10 items
tsv
fragments
fragments
Ansuman Satpathy, Stanford
7.8 GB
validation exempted
hdf5
raw feature barcode matrix
cell by gene in raw feature barcode matrix
Ansuman Satpathy, Stanford
251 MB
validated
tbi
index
index of IGVFFI0627MDWY
Ansuman Satpathy, Stanford
2.1 MB
validated
tsv
cell hashing barcodes
cell hashing barcodes
Ansuman Satpathy, Stanford
883 KB
validated
hdf5
raw feature barcode matrix
cell by gene in raw feature barcode matrix
Ansuman Satpathy, Stanford
275 MB
validated
tsv
cell hashing barcodes
cell hashing barcodes
Ansuman Satpathy, Stanford
720 KB
validated
tbi
index
index of IGVFFI9254IQXZ
Ansuman Satpathy, Stanford
2.2 MB
validated
bed
peaks
GRCh38 peaks
Ansuman Satpathy, Stanford
1.6 MB
validation exempted
bed
peaks
GRCh38 peaks
Ansuman Satpathy, Stanford
1.6 MB
validation exempted
tsv
fragments
fragments
Ansuman Satpathy, Stanford
8.8 GB
validation exempted

File Association Graph

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File Set
File
AnalysisSet
AuxiliarySet
MeasurementSet

Samples

2 items
Sample Terms
Disease Terms
Associated Construct Library Sets
Summary
MultiplexedSample
multiplexed sample: Jurkat cell line, male, Homo sapiens treated with 100 ng/mL phorbol 13-acetate 12-myristate for 4 hours, 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 4 hours; K562 cell line, female, Homo sapiens modified with CRISPRi Sp-dCas9-KOX1-KRAB; ... and 8 more samples
MultiplexedSample
multiplexed sample: Jurkat cell line, male, Homo sapiens treated with 100 ng/mL phorbol 13-acetate 12-myristate for 4 hours, 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 4 hours; K562 cell line, female, Homo sapiens modified with CRISPRi Sp-dCas9-KOX1-KRAB; ... and 8 more samples

Donors

4 items
Aliases
  • igvf:donor_of_Jurkat
male
Homo sapiens
  • igvf:donor_of_teloHAEC
female
Homo sapiens
  • igvf:donor_of_THP1
male
Homo sapiens
  • igvf:donor_of_K562
female
Homo sapiens

MeasurementSet Input File Sets

4 items
Associated Auxiliary Sets
interference single-nucleus ATAC-seq (10x multiome with MULTI-seq)
multiplexed sample: Jurkat cell line, male, Homo sapiens treated with 100 ng/mL phorbol 13-acetate 12-myristate for 4 hours, 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 4 hours; K562 cell line, female, Homo sapiens modified with CRISPRi Sp-dCas9-KOX1-KRAB; ... and 8 more samples
interference single-nucleus ATAC-seq (10x multiome with MULTI-seq)
multiplexed sample: Jurkat cell line, male, Homo sapiens treated with 100 ng/mL phorbol 13-acetate 12-myristate for 4 hours, 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 4 hours; K562 cell line, female, Homo sapiens modified with CRISPRi Sp-dCas9-KOX1-KRAB; ... and 8 more samples
interference single-nucleus RNA sequencing assay (10x multiome with MULTI-seq)
multiplexed sample: Jurkat cell line, male, Homo sapiens treated with 100 ng/mL phorbol 13-acetate 12-myristate for 4 hours, 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 4 hours; K562 cell line, female, Homo sapiens modified with CRISPRi Sp-dCas9-KOX1-KRAB; ... and 8 more samples
interference single-nucleus RNA sequencing assay (10x multiome with MULTI-seq)
multiplexed sample: Jurkat cell line, male, Homo sapiens treated with 100 ng/mL phorbol 13-acetate 12-myristate for 4 hours, 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 4 hours; K562 cell line, female, Homo sapiens modified with CRISPRi Sp-dCas9-KOX1-KRAB; ... and 8 more samples

AuxiliarySet Input File Sets

2 items
Associated Measurement Sets
lipid-conjugated oligo sequencing for interference single-nucleus ATAC-seq (10x multiome with MULTI-seq), interference single-nucleus RNA sequencing assay (10x multiome with MULTI-seq)
multiplexed sample: Jurkat cell line, male, Homo sapiens treated with 100 ng/mL phorbol 13-acetate 12-myristate for 4 hours, 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 4 hours; K562 cell line, female, Homo sapiens modified with CRISPRi Sp-dCas9-KOX1-KRAB; ... and 8 more samples
lipid-conjugated oligo sequencing for interference single-nucleus ATAC-seq (10x multiome with MULTI-seq), interference single-nucleus RNA sequencing assay (10x multiome with MULTI-seq)
multiplexed sample: Jurkat cell line, male, Homo sapiens treated with 100 ng/mL phorbol 13-acetate 12-myristate for 4 hours, 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 4 hours; K562 cell line, female, Homo sapiens modified with CRISPRi Sp-dCas9-KOX1-KRAB; ... and 8 more samples

Attribution

Award
HG011972
Principal Investigator(s)
Contact P.I.
Jesse Engreitz
Lab
Ansuman Satpathy, Stanford