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IGVFDS8898JDCK

released
Aliases
ansuman-satpathy:igvf5_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 - H1 gastruloids, WTC11 NGN2 neurons, H9 neuron differentiation, HEK293T
Workflows
Samples
H9, HEK293T, H1-hESC, GM25256 (WTC-11) cell line and differentiated cell specimen and gastruloid and multiplexed sample
Protocols

Files

20 items
hdf5
raw feature barcode matrix
cell by gene in raw feature barcode matrix
Ansuman Satpathy, Stanford
138 MB
validated
bed
peaks
GRCh38 peaks
Ansuman Satpathy, Stanford
2.3 MB
validation exempted
tsv
fragments
fragments
Ansuman Satpathy, Stanford
5.9 GB
validation exempted
tbi
index
index of IGVFFI8232SKBR
Ansuman Satpathy, Stanford
1.8 MB
validated
tsv
cell hashing barcodes
cell hashing barcodes
Ansuman Satpathy, Stanford
403 KB
validated
hdf5
raw feature barcode matrix
cell by gene in raw feature barcode matrix
Ansuman Satpathy, Stanford
163 MB
validated
bed
peaks
GRCh38 peaks
Ansuman Satpathy, Stanford
2.4 MB
validation exempted
tsv
cell hashing barcodes
cell hashing barcodes
Ansuman Satpathy, Stanford
479 KB
validated
tsv
fragments
fragments
Ansuman Satpathy, Stanford
6.4 GB
validation exempted
hdf5
raw feature barcode matrix
cell by gene in raw feature barcode matrix
Ansuman Satpathy, Stanford
200 MB
validated

File Association Graph

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File Set
File
AnalysisSet
AuxiliarySet
MeasurementSet

Samples

4 items
Sample Terms
Disease Terms
Associated Construct Library Sets
Summary
MultiplexedSample
multiplexed sample: H9 differentiated cell specimen induced to neuron for 6 days, female, Homo sapiens; H9 differentiated cell specimen induced to neuron for 6 days, female, Homo sapiens; ... and 6 more samples
MultiplexedSample
multiplexed sample: H9 differentiated cell specimen induced to neuron for 6 days, female, Homo sapiens; H9 differentiated cell specimen induced to neuron for 6 days, female, Homo sapiens; ... and 6 more samples
MultiplexedSample
multiplexed sample: H9 differentiated cell specimen induced to neuron for 6 days, female, Homo sapiens; H9 differentiated cell specimen induced to neuron for 6 days, female, Homo sapiens; ... and 6 more samples
MultiplexedSample
multiplexed sample: H9 differentiated cell specimen induced to neuron for 6 days, female, Homo sapiens; H9 differentiated cell specimen induced to neuron for 6 days, female, Homo sapiens; ... and 6 more samples

Donors

4 items
Aliases
  • igvf:donor_of_HEK293T
female
Homo sapiens
  • igvf:donor_of_WTC11
male
Homo sapiens
  • igvf:donor_of_H9
female
Homo sapiens
  • igvf:donor_of_H1
male
Homo sapiens

MeasurementSet Input File Sets

8 items
Associated Auxiliary Sets
single-nucleus ATAC-seq (10x multiome with MULTI-seq)
multiplexed sample: H9 differentiated cell specimen induced to neuron for 6 days, female, Homo sapiens; H9 differentiated cell specimen induced to neuron for 6 days, female, Homo sapiens; ... and 6 more samples
single-nucleus ATAC-seq (10x multiome with MULTI-seq)
multiplexed sample: H9 differentiated cell specimen induced to neuron for 6 days, female, Homo sapiens; H9 differentiated cell specimen induced to neuron for 6 days, female, Homo sapiens; ... and 6 more samples
single-nucleus ATAC-seq (10x multiome with MULTI-seq)
multiplexed sample: H9 differentiated cell specimen induced to neuron for 6 days, female, Homo sapiens; H9 differentiated cell specimen induced to neuron for 6 days, female, Homo sapiens; ... and 6 more samples
single-nucleus ATAC-seq (10x multiome with MULTI-seq)
multiplexed sample: H9 differentiated cell specimen induced to neuron for 6 days, female, Homo sapiens; H9 differentiated cell specimen induced to neuron for 6 days, female, Homo sapiens; ... and 6 more samples
single-nucleus RNA sequencing assay (10x multiome with MULTI-seq)
multiplexed sample: H9 differentiated cell specimen induced to neuron for 6 days, female, Homo sapiens; H9 differentiated cell specimen induced to neuron for 6 days, female, Homo sapiens; ... and 6 more samples
single-nucleus RNA sequencing assay (10x multiome with MULTI-seq)
multiplexed sample: H9 differentiated cell specimen induced to neuron for 6 days, female, Homo sapiens; H9 differentiated cell specimen induced to neuron for 6 days, female, Homo sapiens; ... and 6 more samples
single-nucleus RNA sequencing assay (10x multiome with MULTI-seq)
multiplexed sample: H9 differentiated cell specimen induced to neuron for 6 days, female, Homo sapiens; H9 differentiated cell specimen induced to neuron for 6 days, female, Homo sapiens; ... and 6 more samples
single-nucleus RNA sequencing assay (10x multiome with MULTI-seq)
multiplexed sample: H9 differentiated cell specimen induced to neuron for 6 days, female, Homo sapiens; H9 differentiated cell specimen induced to neuron for 6 days, female, Homo sapiens; ... and 6 more samples

AuxiliarySet Input File Sets

4 items
Associated Measurement Sets
lipid-conjugated oligo sequencing for single-nucleus ATAC-seq (10x multiome with MULTI-seq), single-nucleus RNA sequencing assay (10x multiome with MULTI-seq)
multiplexed sample: H9 differentiated cell specimen induced to neuron for 6 days, female, Homo sapiens; H9 differentiated cell specimen induced to neuron for 6 days, female, Homo sapiens; ... and 6 more samples
lipid-conjugated oligo sequencing for single-nucleus RNA sequencing assay (10x multiome with MULTI-seq), single-nucleus ATAC-seq (10x multiome with MULTI-seq)
multiplexed sample: H9 differentiated cell specimen induced to neuron for 6 days, female, Homo sapiens; H9 differentiated cell specimen induced to neuron for 6 days, female, Homo sapiens; ... and 6 more samples
lipid-conjugated oligo sequencing for single-nucleus RNA sequencing assay (10x multiome with MULTI-seq), single-nucleus ATAC-seq (10x multiome with MULTI-seq)
multiplexed sample: H9 differentiated cell specimen induced to neuron for 6 days, female, Homo sapiens; H9 differentiated cell specimen induced to neuron for 6 days, female, Homo sapiens; ... and 6 more samples
lipid-conjugated oligo sequencing for single-nucleus RNA sequencing assay (10x multiome with MULTI-seq), single-nucleus ATAC-seq (10x multiome with MULTI-seq)
multiplexed sample: H9 differentiated cell specimen induced to neuron for 6 days, female, Homo sapiens; H9 differentiated cell specimen induced to neuron for 6 days, female, Homo sapiens; ... and 6 more samples

Attribution

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