{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS7268XYPD/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7268XYPD",
"aliases": [
"charles-gersbach:analysis-set-crispra-region3-mouse-hl1-targeted-hicar-rep3-cool"
],
"assay_titles": [
"HiCAR"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "Analysis set [IGVFDS7268XYPD](/analysis-sets/IGVFDS7268XYPD/) 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/IGVFDS7268XYPD/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM5017HPIL](/in-vitro-systems/IGVFSM5017HPIL/) 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/IGVFSM5017HPIL/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM5017HPIL](/in-vitro-systems/IGVFSM5017HPIL/) 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/IGVFSM5017HPIL/"
}
]
},
"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/IGVFDS8122GWMC/",
"accession": "IGVFDS8122GWMC",
"file_set_type": "guide library",
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI7693PBDH/",
"accession": "IGVFFI7693PBDH",
"content_type": "guide RNA sequences",
"status": "released",
"summary": "GRCm39 guide RNA sequences"
}
],
"status": "released",
"summary": "guide (sgRNA) library targeting accessible genome regions in a genomic locus"
}
],
"control_for": [],
"controlled_access": false,
"creation_timestamp": "2024-11-07T15:46:56.031331+00:00",
"data_use_limitation_summaries": [
"No limitations"
],
"donors": [
{
"@id": "/rodent-donors/IGVFDO1434JYIN/",
"accession": "IGVFDO1434JYIN",
"aliases": [
"charles-gersbach:mouse-donor-HL-1"
],
"sex": "female",
"status": "released",
"taxa": "Mus musculus"
}
],
"file_set_type": "intermediate analysis",
"files": [
{
"@id": "/matrix-files/IGVFFI2377NFOC/",
"accession": "IGVFFI2377NFOC",
"aliases": [
"charles-gersbach:matrix-file-crispra-region3-mouse-hl1-targeted-hicar-rep3-mcool"
],
"content_type": "contact matrix",
"creation_timestamp": "2024-11-07T16:07:41.476505+00:00",
"file_format": "mcool",
"file_size": 49639434,
"href": "/matrix-files/IGVFFI2377NFOC/@@download/IGVFFI2377NFOC.mcool",
"s3_uri": "s3://igvf-files/2024/11/07/6463fbb6-bf2b-4a32-b38c-f8a6ed0312dd/IGVFFI2377NFOC.mcool",
"status": "released",
"submitted_file_name": "/hpc/group/gersbachlab/tda17/IGVF_data_files/HiCAR/output/cooler/mouse/HL1_TA446_CA_3_ctrl.1000.mcool",
"upload_status": "validated"
},
{
"@id": "/matrix-files/IGVFFI1509VTYC/",
"accession": "IGVFFI1509VTYC",
"aliases": [
"charles-gersbach:matrix-file-crispra-region3-mouse-hl1-targeted-hicar-rep3-cool"
],
"content_type": "contact matrix",
"creation_timestamp": "2024-11-07T16:07:39.782635+00:00",
"file_format": "cool",
"file_size": 10900127,
"href": "/matrix-files/IGVFFI1509VTYC/@@download/IGVFFI1509VTYC.cool",
"s3_uri": "s3://igvf-files/2024/11/07/aad36397-86bb-43fe-b1b7-64c81f0a30da/IGVFFI1509VTYC.cool",
"status": "released",
"submitted_file_name": "/hpc/group/gersbachlab/tda17/IGVF_data_files/HiCAR/output/cooler/mouse/HL1_TA446_CA_3_ctrl.1000.cool",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/measurement-sets/IGVFDS1873QGHK/",
"accession": "IGVFDS1873QGHK",
"aliases": [
"charles-gersbach:measurement-set-crispra-region3-mouse-hl1-targeted-hicar-rep3"
],
"file_set_type": "experimental data",
"status": "released"
}
],
"input_for": [
"/analysis-sets/IGVFDS0872LUHP/"
],
"lab": {
"@id": "/labs/charles-gersbach/",
"title": "Charles Gersbach, Duke"
},
"protocols": [
"https://www.protocols.io/view/hicar-for-mouse-hl-1-cells-following-enhancer-pert-36wgqn2yygk5"
],
"release_timestamp": "2024-12-13T19:43:28.235300+00:00",
"sample_summary": "Mus musculus HL-1 cell line, transfected with a guide library",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5017HPIL/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5017HPIL",
"aliases": [
"charles-gersbach:in-vitro-system-ccrispra-region3-mouse-hl1-targeted-hicar-rep3"
],
"classifications": [
"cell line"
],
"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_0022835/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "HL-1",
"term_name": "HL-1"
}
],
"status": "released",
"summary": "Mus musculus C57BL/6J (female) HL-1 cell line transfected with a guide library",
"taxa": "Mus musculus"
}
],
"schema_version": "9",
"status": "released",
"submitted_by": {
"@id": "/users/3782ce69-0e9f-4b46-91f9-4578139785c7/",
"title": "Ruhi Rai"
},
"submitted_files_timestamp": "2024-11-07T16:07:39.782635+00:00",
"summary": "HiCAR: contact matrix",
"uuid": "242832d1-4db0-4f8b-9eb6-1762bd3f7d06",
"workflows": [
{
"@id": "/workflows/IGVFWF1709OHTV/",
"accession": "IGVFWF1709OHTV",
"name": "nf-core HiCAR Pipeline",
"status": "released",
"uniform_pipeline": false
}
]
}