{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS0872LUHP/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0872LUHP",
"aliases": [
"charles-gersbach:analysis-set-crispra-HL1-region3-DEanalysis"
],
"assay_titles": [
"HiCAR"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM6964SBRF](/in-vitro-systems/IGVFSM6964SBRF/) 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/IGVFSM6964SBRF/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM1004RIDZ](/in-vitro-systems/IGVFSM1004RIDZ/) 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/IGVFSM1004RIDZ/"
},
{
"category": "missing publication",
"detail": "Analysis set [IGVFDS0872LUHP](/analysis-sets/IGVFDS0872LUHP/) 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/IGVFDS0872LUHP/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM8571KCNL](/in-vitro-systems/IGVFSM8571KCNL/) 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/IGVFSM8571KCNL/"
},
{
"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/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM7656WGBF](/in-vitro-systems/IGVFSM7656WGBF/) 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/IGVFSM7656WGBF/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM3147FFHB](/in-vitro-systems/IGVFSM3147FFHB/) 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/IGVFSM3147FFHB/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM6964SBRF](/in-vitro-systems/IGVFSM6964SBRF/) 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/IGVFSM6964SBRF/"
},
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM1004RIDZ](/in-vitro-systems/IGVFSM1004RIDZ/) 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/IGVFSM1004RIDZ/"
},
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM8571KCNL](/in-vitro-systems/IGVFSM8571KCNL/) 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/IGVFSM8571KCNL/"
},
{
"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/"
},
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM7656WGBF](/in-vitro-systems/IGVFSM7656WGBF/) 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/IGVFSM7656WGBF/"
},
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM3147FFHB](/in-vitro-systems/IGVFSM3147FFHB/) 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/IGVFSM3147FFHB/"
}
]
},
"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/IGVFDS4536EZHP/",
"accession": "IGVFDS4536EZHP",
"file_set_type": "guide library",
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI5055KQHH/",
"accession": "IGVFFI5055KQHH",
"content_type": "guide RNA sequences",
"status": "released",
"summary": "GRCm39 guide RNA sequences"
}
],
"status": "released",
"summary": "non-targeting guide (sgRNA) library"
},
{
"@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": "2024-10-29T19:51:50.715592+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": "principal analysis",
"files": [
{
"@id": "/tabular-files/IGVFFI3183CEXF/",
"accession": "IGVFFI3183CEXF",
"aliases": [
"charles-gersbach:tabular-file-crispra-HL1-region3-DEanalysis"
],
"assembly": "GRCm39",
"content_type": "differential chromatin contact quantifications",
"controlled_access": false,
"creation_timestamp": "2024-10-30T14:59:46.701642+00:00",
"file_format": "csv",
"file_size": 6817,
"href": "/tabular-files/IGVFFI3183CEXF/@@download/IGVFFI3183CEXF.csv.gz",
"s3_uri": "s3://igvf-files/2024/10/30/5b4e954a-9f4b-4df8-9863-be3cf12025e1/IGVFFI3183CEXF.csv.gz",
"status": "released",
"submitted_file_name": "/hpc/group/gersbachlab/tda17/IGVF_data_files/HiCAR/output/Count_matrix_and_DESeq2/HL1_Region3_active_vs_nontarget_ctrl_Union_10kb_DE_results.csv.gz",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI4745FFZE/",
"accession": "IGVFFI4745FFZE",
"aliases": [
"charles-gersbach:tabular-file-crispra-HL1-region3-count"
],
"assembly": "GRCm39",
"content_type": "bin paired count",
"controlled_access": false,
"creation_timestamp": "2024-10-30T14:59:45.338127+00:00",
"file_format": "tsv",
"file_size": 2108,
"href": "/tabular-files/IGVFFI4745FFZE/@@download/IGVFFI4745FFZE.tsv.gz",
"s3_uri": "s3://igvf-files/2024/10/30/b7a32a9f-0b7c-4225-8a74-cc5b889ad5a6/IGVFFI4745FFZE.tsv.gz",
"status": "released",
"submitted_file_name": "/hpc/group/gersbachlab/tda17/IGVF_data_files/HiCAR/output/Count_matrix_and_DESeq2/HL1_Region3_active_vs_nontarget_ctrl_Union_10kb_count_mat.tsv.gz",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/analysis-sets/IGVFDS3159CKGQ/",
"accession": "IGVFDS3159CKGQ",
"aliases": [
"charles-gersbach:analysis-set-crispra-region3-mouse-hl1-targeted-hicar-rep1-cool"
],
"file_set_type": "intermediate analysis",
"status": "released"
},
{
"@id": "/analysis-sets/IGVFDS2562CZKX/",
"accession": "IGVFDS2562CZKX",
"aliases": [
"charles-gersbach:analysis-set-crispra-control-mouse-hl1-targeted-hicar-rep2-cool"
],
"file_set_type": "intermediate analysis",
"status": "released"
},
{
"@id": "/analysis-sets/IGVFDS7268XYPD/",
"accession": "IGVFDS7268XYPD",
"aliases": [
"charles-gersbach:analysis-set-crispra-region3-mouse-hl1-targeted-hicar-rep3-cool"
],
"file_set_type": "intermediate analysis",
"status": "released"
},
{
"@id": "/analysis-sets/IGVFDS0318CFLU/",
"accession": "IGVFDS0318CFLU",
"aliases": [
"charles-gersbach:analysis-set-crispra-control-mouse-hl1-targeted-hicar-rep1-cool"
],
"file_set_type": "intermediate analysis",
"status": "released"
},
{
"@id": "/analysis-sets/IGVFDS2723TEYB/",
"accession": "IGVFDS2723TEYB",
"aliases": [
"charles-gersbach:analysis-set-crispra-control-mouse-hl1-targeted-hicar-rep3-cool"
],
"file_set_type": "intermediate analysis",
"status": "released"
},
{
"@id": "/analysis-sets/IGVFDS4066YEFI/",
"accession": "IGVFDS4066YEFI",
"aliases": [
"charles-gersbach:analysis-set-crispra-region3-mouse-hl1-targeted-hicar-rep2-cool"
],
"file_set_type": "intermediate analysis",
"status": "released"
}
],
"input_for": [],
"lab": {
"@id": "/labs/charles-gersbach/",
"title": "Charles Gersbach, Duke"
},
"protocols": [],
"release_timestamp": "2024-12-13T19:43:27.453452+00:00",
"sample_summary": "Mus musculus HL-1 cell line, transfected with a guide library",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8571KCNL/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8571KCNL",
"aliases": [
"charles-gersbach:in-vitro-system-crispra-control-mouse-hl1-targeted-hicar-rep2"
],
"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"
},
{
"@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": [
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],
"institutional_certificates": [
{
"@id": "/institutional-certificates/a62cea9b-2ae0-44e8-a6d6-81f419c56c71/",
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}
],
"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"
},
{
"@id": "/in-vitro-systems/IGVFSM7656WGBF/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7656WGBF",
"aliases": [
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"classifications": [
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],
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{
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}
],
"sample_terms": [
{
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"OntologyTerm",
"Item"
],
"status": "released",
"summary": "HL-1",
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}
],
"status": "released",
"summary": "Mus musculus C57BL/6J (female) HL-1 cell line transfected with a guide library",
"taxa": "Mus musculus"
},
{
"@id": "/in-vitro-systems/IGVFSM3147FFHB/",
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"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3147FFHB",
"aliases": [
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"classifications": [
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],
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{
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}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0022835/",
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],
"status": "released",
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}
],
"status": "released",
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"taxa": "Mus musculus"
},
{
"@id": "/in-vitro-systems/IGVFSM6964SBRF/",
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"Sample",
"Item"
],
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"classifications": [
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"institutional_certificates": [
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}
],
"sample_terms": [
{
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"Item"
],
"status": "released",
"summary": "HL-1",
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}
],
"status": "released",
"summary": "Mus musculus C57BL/6J (female) HL-1 cell line transfected with a guide library",
"taxa": "Mus musculus"
},
{
"@id": "/in-vitro-systems/IGVFSM1004RIDZ/",
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"Sample",
"Item"
],
"accession": "IGVFSM1004RIDZ",
"aliases": [
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"classifications": [
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],
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"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0022835/",
"@type": [
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"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": "2024-10-30T14:59:45.338127+00:00",
"summary": "HiCAR: bin paired count, differential chromatin contact quantifications",
"uuid": "3e081d4d-f995-4962-a315-a1defb8a8219",
"workflows": [
{
"@id": "/workflows/IGVFWF2849QJOS/",
"accession": "IGVFWF2849QJOS",
"name": "Gersbach HiCAR Quantification Workflow",
"status": "released",
"uniform_pipeline": false
}
]
}