{
"@context": "/terms/",
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],
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"aliases": [
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],
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],
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{
"category": "missing publication",
"detail": "In vitro system [IGVFSM6234HZRL](/in-vitro-systems/IGVFSM6234HZRL/) 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/IGVFSM6234HZRL/"
},
{
"category": "missing publication",
"detail": "Analysis set [IGVFDS4526ROPM](/analysis-sets/IGVFDS4526ROPM/) 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/IGVFDS4526ROPM/"
}
]
},
"award": {
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"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/IGVFDS7331UHMB/",
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"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": "2024-11-07T15:46:28.197883+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",
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{
"@id": "/matrix-files/IGVFFI2379IGYT/",
"accession": "IGVFFI2379IGYT",
"aliases": [
"charles-gersbach:matrix-file-crispra-control-0umETt1-ipsc-cm-targeted-hicar-rep1-mcool"
],
"content_type": "contact matrix",
"creation_timestamp": "2024-11-07T16:06:49.176989+00:00",
"derived_from": [
"/sequence-files/IGVFFI9934OVTR/",
"/sequence-files/IGVFFI4752WVEQ/"
],
"file_format": "mcool",
"file_size": 40794220,
"href": "/matrix-files/IGVFFI2379IGYT/@@download/IGVFFI2379IGYT.mcool",
"md5sum": "d014e946d5a31109a1b1c39290e997d2",
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"status": "released",
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"upload_status": "validated"
},
{
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"derived_from": [
"/matrix-files/IGVFFI2379IGYT/"
],
"file_format": "cool",
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"md5sum": "215e31a02a013b76fa054ec2b416cfd9",
"s3_uri": "s3://igvf-files/2024/11/07/e51693dd-9ef2-4791-ad81-49db050789f7/IGVFFI2160BPKW.cool",
"status": "released",
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"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/measurement-sets/IGVFDS0456TVFV/",
"accession": "IGVFDS0456TVFV",
"aliases": [
"charles-gersbach:measurement-set-crispra-control-0umETt1-ipsc-cm-targeted-hicar-rep1"
],
"file_set_type": "experimental data",
"status": "released"
}
],
"input_for": [
"/analysis-sets/IGVFDS2248ZJTA/",
"/analysis-sets/IGVFDS4356CHAN/"
],
"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": "2024-12-13T19:43:45.743485+00:00",
"sample_summary": "Homo sapiens GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell, at 42 day(s) post change, transfected with a guide library",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM6234HZRL/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6234HZRL",
"aliases": [
"charles-gersbach:in-vitro-system-crispra-control-0umET1-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": [
{
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"@type": [
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"OntologyTerm",
"Item"
],
"aliases": [
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],
"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 transduced (lentivirus) with a guide library",
"targeted_sample_term": {
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"status": "released",
"term_name": "cardiac muscle cell"
},
"taxa": "Homo sapiens"
}
],
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"status": "released",
"submitted_by": {
"@id": "/users/3782ce69-0e9f-4b46-91f9-4578139785c7/",
"title": "Ruhi Rai"
},
"submitted_files_timestamp": "2024-11-07T16:06:47.631741+00:00",
"summary": "CRISPR HiCAR: contact matrix",
"uuid": "c0f146e9-e2cc-4a1b-af1a-c8acbccbadbd",
"workflows": [
{
"@id": "/workflows/IGVFWF1709OHTV/",
"accession": "IGVFWF1709OHTV",
"name": "nf-core HiCAR Pipeline",
"status": "released",
"uniform_pipeline": false
}
]
}