{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS2248ZJTA/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2248ZJTA",
"aliases": [
"charles-gersbach:analysis-set-crispra-stim-ctrl-NT-DEanalysis"
],
"assay_titles": [
"HiCAR"
],
"audit": {
"INTERNAL_ACTION": [
{
"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": "In vitro system [IGVFSM7176NKKR](/in-vitro-systems/IGVFSM7176NKKR/) 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/IGVFSM7176NKKR/"
},
{
"category": "missing publication",
"detail": "Analysis set [IGVFDS2248ZJTA](/analysis-sets/IGVFDS2248ZJTA/) 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/IGVFDS2248ZJTA/"
},
{
"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": "In vitro system [IGVFSM9382KDYU](/in-vitro-systems/IGVFSM9382KDYU/) 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/IGVFSM9382KDYU/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM6234HZRL](/in-vitro-systems/IGVFSM6234HZRL/) 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/IGVFSM6234HZRL/"
},
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM7176NKKR](/in-vitro-systems/IGVFSM7176NKKR/) 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/IGVFSM7176NKKR/"
},
{
"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/"
},
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM9382KDYU](/in-vitro-systems/IGVFSM9382KDYU/) 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/IGVFSM9382KDYU/"
}
]
},
"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/IGVFDS7331UHMB/",
"accession": "IGVFDS7331UHMB",
"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"
},
{
"@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": "2024-10-29T19:51:40.476288+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": "principal analysis",
"files": [
{
"@id": "/tabular-files/IGVFFI2054HSCC/",
"accession": "IGVFFI2054HSCC",
"aliases": [
"charles-gersbach:tabular-file-crispra-stim-ctrl-NT-DEanalysis"
],
"assembly": "GRCh38",
"content_type": "differential chromatin contact quantifications",
"controlled_access": false,
"creation_timestamp": "2024-10-30T14:59:32.328514+00:00",
"file_format": "csv",
"file_size": 7451,
"href": "/tabular-files/IGVFFI2054HSCC/@@download/IGVFFI2054HSCC.csv.gz",
"s3_uri": "s3://igvf-files/2024/10/30/88fd5b38-39ed-45e8-bf35-9d2a27b592a3/IGVFFI2054HSCC.csv.gz",
"status": "released",
"submitted_file_name": "/hpc/group/gersbachlab/tda17/IGVF_data_files/HiCAR/output/Count_matrix_and_DESeq2/CRISPRa.stim_vs_ctrl_Union_in_NT_10kb_DE_results.csv.gz",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI2294VFGH/",
"accession": "IGVFFI2294VFGH",
"aliases": [
"charles-gersbach:tabular-file-crispra-stim-ctrl-NT-count"
],
"assembly": "GRCh38",
"content_type": "bin paired count",
"controlled_access": false,
"creation_timestamp": "2024-10-30T14:59:30.111147+00:00",
"file_format": "tsv",
"file_size": 1732,
"href": "/tabular-files/IGVFFI2294VFGH/@@download/IGVFFI2294VFGH.tsv.gz",
"s3_uri": "s3://igvf-files/2024/10/30/c560e9b5-2a50-4cc9-a892-d250f09d8485/IGVFFI2294VFGH.tsv.gz",
"status": "released",
"submitted_file_name": "/hpc/group/gersbachlab/tda17/IGVF_data_files/HiCAR/output/Count_matrix_and_DESeq2/CRISPRa.stim_vs_ctrl_Union_in_NT_10kb_count_mat_CRISPRi_range_res_10kb.tsv.gz",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/analysis-sets/IGVFDS8055FNVD/",
"accession": "IGVFDS8055FNVD",
"aliases": [
"charles-gersbach:analysis-set-crispra-control-0umETt1-ipsc-cm-targeted-hicar-rep2-cool"
],
"file_set_type": "intermediate analysis",
"status": "released"
},
{
"@id": "/analysis-sets/IGVFDS1166CYWU/",
"accession": "IGVFDS1166CYWU",
"aliases": [
"charles-gersbach:analysis-set-crispra-control-1umET1-ipsc-cm-targeted-hicar-rep1-cool"
],
"file_set_type": "intermediate analysis",
"status": "released"
},
{
"@id": "/analysis-sets/IGVFDS0561MJAA/",
"accession": "IGVFDS0561MJAA",
"aliases": [
"charles-gersbach:analysis-set-crispra-control-1umET1-ipsc-cm-targeted-hicar-rep2-cool"
],
"file_set_type": "intermediate analysis",
"status": "released"
},
{
"@id": "/analysis-sets/IGVFDS4526ROPM/",
"accession": "IGVFDS4526ROPM",
"aliases": [
"charles-gersbach:analysis-set-crispra-control-0umETt1-ipsc-cm-targeted-hicar-rep1-cool"
],
"file_set_type": "intermediate analysis",
"status": "released"
}
],
"input_for": [],
"lab": {
"@id": "/labs/charles-gersbach/",
"title": "Charles Gersbach, Duke"
},
"protocols": [],
"release_timestamp": "2024-12-13T19:44:04.976766+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/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": [
{
"@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 transfected with a guide library",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000746/",
"status": "released",
"term_name": "cardiac muscle cell"
},
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM7176NKKR/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7176NKKR",
"aliases": [
"charles-gersbach:in-vitro-system-crispra-control-1umET1-ipsc-cm-targeted-hicar-rep2"
],
"classifications": [
"differentiated cell specimen"
],
"institutional_certificates": [
{
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"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"
}
]
},
{
"@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"
}
]
},
{
"@id": "/in-vitro-systems/IGVFSM9382KDYU/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9382KDYU",
"aliases": [
"charles-gersbach:in-vitro-system-crispra-control-0umET1-ipsc-cm-targeted-hicar-rep2"
],
"classifications": [
"differentiated cell specimen"
],
"institutional_certificates": [
{
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"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 transfected with a guide library",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000746/",
"status": "released",
"term_name": "cardiac muscle cell"
},
"taxa": "Homo sapiens"
}
],
"schema_version": "9",
"status": "released",
"submitted_by": {
"@id": "/users/3782ce69-0e9f-4b46-91f9-4578139785c7/",
"title": "Ruhi Rai"
},
"submitted_files_timestamp": "2024-10-30T14:59:30.111147+00:00",
"summary": "HiCAR: bin paired count, differential chromatin contact quantifications",
"uuid": "41e2d33f-d694-4ca7-977f-ba9c66e6215a",
"workflows": [
{
"@id": "/workflows/IGVFWF2849QJOS/",
"accession": "IGVFWF2849QJOS",
"name": "Gersbach HiCAR Quantification Workflow",
"status": "released",
"uniform_pipeline": false
}
]
}