{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS1166CYWU/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1166CYWU",
"aliases": [
"charles-gersbach:analysis-set-crispra-control-1umET1-ipsc-cm-targeted-hicar-rep1-cool"
],
"assay_titles": [
"HiCAR"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM2698DFOT](/in-vitro-systems/IGVFSM2698DFOT/) has no `publications`. Released and archived samples are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_sample_missing_publication",
"path": "/in-vitro-systems/IGVFSM2698DFOT/"
},
{
"category": "missing publication",
"detail": "Analysis set [IGVFDS1166CYWU](/analysis-sets/IGVFDS1166CYWU/) has no `publications`. Released and archived file sets are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_file_set_missing_publication",
"path": "/analysis-sets/IGVFDS1166CYWU/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM2698DFOT](/in-vitro-systems/IGVFSM2698DFOT/) has `construct_library_sets` but is missing `nucleic_acid_delivery`. Samples linked to construct library sets are expected to specify nucleic acid delivery method.",
"level": 40,
"level_name": "WARNING",
"name": "audit_missing_nucleic_acid_delivery",
"path": "/in-vitro-systems/IGVFSM2698DFOT/"
}
]
},
"award": {
"@id": "/awards/HG012053/",
"component": "functional characterization",
"contact_pi": {
"@id": "/users/5d329c0e-3ea9-49bf-9bb9-844a53a882c0/",
"title": "Charles Gersbach"
},
"title": "High-Throughput Functional Annotation of Gene Regulatory Elements and Variants Critical to Complex Cellular Phenotypes"
},
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS6209EFIL/",
"accession": "IGVFDS6209EFIL",
"file_set_type": "guide library",
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI7739QJBH/",
"accession": "IGVFFI7739QJBH",
"content_type": "guide RNA sequences",
"status": "released",
"summary": "GRCh38 guide RNA sequences"
}
],
"status": "released",
"summary": "non-targeting guide (sgRNA) library"
}
],
"control_for": [],
"controlled_access": false,
"creation_timestamp": "2024-11-07T15:46:38.292934+00:00",
"data_use_limitation_summaries": [
"No limitations"
],
"donors": [
{
"@id": "/human-donors/IGVFDO1756PPKO/",
"accession": "IGVFDO1756PPKO",
"aliases": [
"igvf:donor_of_WTC11"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "intermediate analysis",
"files": [
{
"@id": "/matrix-files/IGVFFI1058WSVT/",
"accession": "IGVFFI1058WSVT",
"aliases": [
"charles-gersbach:matrix-file-crispra-control-1umET1-ipsc-cm-targeted-hicar-rep1-mcool"
],
"content_type": "contact matrix",
"creation_timestamp": "2024-11-07T16:07:08.704930+00:00",
"file_format": "mcool",
"file_size": 36593102,
"href": "/matrix-files/IGVFFI1058WSVT/@@download/IGVFFI1058WSVT.mcool",
"s3_uri": "s3://igvf-files/2024/11/07/9b96b310-8c66-418e-a1d4-6b0e60a1d7db/IGVFFI1058WSVT.mcool",
"status": "released",
"submitted_file_name": "/hpc/group/gersbachlab/tda17/IGVF_data_files/HiCAR/output/cooler/human/VP64_NT_1_stim.1000.mcool",
"upload_status": "validated"
},
{
"@id": "/matrix-files/IGVFFI4306VSRX/",
"accession": "IGVFFI4306VSRX",
"aliases": [
"charles-gersbach:matrix-file-crispra-control-1umET1-ipsc-cm-targeted-hicar-rep1-cool"
],
"content_type": "contact matrix",
"creation_timestamp": "2024-11-07T16:07:07.165573+00:00",
"file_format": "cool",
"file_size": 8252751,
"href": "/matrix-files/IGVFFI4306VSRX/@@download/IGVFFI4306VSRX.cool",
"s3_uri": "s3://igvf-files/2024/11/07/2596f84a-45a2-4898-a33a-990abf11bf67/IGVFFI4306VSRX.cool",
"status": "released",
"submitted_file_name": "/hpc/group/gersbachlab/tda17/IGVF_data_files/HiCAR/output/cooler/human/VP64_NT_1_stim.1000.cool",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/measurement-sets/IGVFDS2114RIWO/",
"accession": "IGVFDS2114RIWO",
"aliases": [
"charles-gersbach:measurement-set-crispra-control-1umET1-ipsc-cm-targeted-hicar-rep1"
],
"file_set_type": "experimental data",
"status": "released"
}
],
"input_for": [
"/analysis-sets/IGVFDS2248ZJTA/",
"/analysis-sets/IGVFDS7797WATU/"
],
"lab": {
"@id": "/labs/charles-gersbach/",
"title": "Charles Gersbach, Duke"
},
"protocols": [
"https://www.protocols.io/view/hicar-for-human-ipsc-cm-following-enhancer-perturb-3byl49mdrgo5"
],
"release_timestamp": "2024-12-13T19:43:54.638270+00:00",
"sample_summary": "Homo sapiens GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell, at 42 day(s) post change, perturbed with 1 μM Endothelin-1 for 3 days, transfected with a guide library",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2698DFOT/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2698DFOT",
"aliases": [
"charles-gersbach:in-vitro-system-crispra-control-1umET1-ipsc-cm-targeted-hicar-rep1"
],
"classifications": [
"differentiated cell specimen"
],
"institutional_certificates": [
{
"@id": "/institutional-certificates/a62cea9b-2ae0-44e8-a6d6-81f419c56c71/",
"certificate_identifier": "IP117-03",
"controlled_access": false,
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:WTC11"
],
"status": "released",
"summary": "GM25256 (WTC-11)",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "released",
"summary": "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",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000746/",
"status": "released",
"term_name": "cardiac muscle cell"
},
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/bbe5df8d-a9e2-4a99-8942-9b3b7d12c605/",
"purpose": "perturbation",
"status": "released",
"summary": "Treatment of 1 μM Endothelin-1 for 3 days",
"treatment_type": "chemical"
}
]
}
],
"schema_version": "9",
"status": "released",
"submitted_by": {
"@id": "/users/3782ce69-0e9f-4b46-91f9-4578139785c7/",
"title": "Ruhi Rai"
},
"submitted_files_timestamp": "2024-11-07T16:07:07.165573+00:00",
"summary": "HiCAR: contact matrix",
"uuid": "0e5d8aad-2fe0-487d-a7ff-b31d2be83a1e",
"workflows": [
{
"@id": "/workflows/IGVFWF1709OHTV/",
"accession": "IGVFWF1709OHTV",
"name": "nf-core HiCAR Pipeline",
"status": "released",
"uniform_pipeline": false
}
]
}