{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6748EEVW/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6748EEVW",
"aliases": [
"charles-gersbach:measurement-set-crispra-control-1umET1-ipsc-cm-targeted-hicar-rep2"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002440/",
"assay_slims": [
"3D chromatin structure"
],
"status": "released",
"term_name": "Hi-C assay"
},
"audit": {
"INTERNAL_ACTION": [
{
"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": "Measurement set [IGVFDS6748EEVW](/measurement-sets/IGVFDS6748EEVW/) 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": "/measurement-sets/IGVFDS6748EEVW/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS6748EEVW](/measurement-sets/IGVFDS6748EEVW/) has sequence file(s): [IGVFFI1238FADY](/sequence-files/IGVFFI1238FADY/), [IGVFFI6320ENYC](/sequence-files/IGVFFI6320ENYC/) which do not have any `seqspecs`. Sequence files in a file set associated with bulk data are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS6748EEVW/"
}
],
"WARNING": [
{
"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/"
}
]
},
"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": "2024-10-23T19:20:03.919690+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"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI1238FADY/",
"accession": "IGVFFI1238FADY",
"aliases": [
"charles-gersbach:measurement-set-crispra-control-1umET1-ipsc-cm-targeted-hicar-rep2-R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-10-23T19:29:36.739996+00:00",
"file_format": "fastq",
"file_size": 1200217354,
"href": "/sequence-files/IGVFFI1238FADY/@@download/IGVFFI1238FADY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/10/23/e2b150ad-8f58-4501-aa90-ba8fe12fda0c/IGVFFI1238FADY.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0010963/",
"status": "released",
"term_name": "Illumina NextSeq 2000"
},
"status": "released",
"submitted_file_name": "/hpc/group/gersbachlab/tda17/IGVF_data_files/HiCAR/fastq/crispra_human/crispra_hicar_human_fastq/H_vp64_r2_NT_3_1uMET1_ds.93b658e4765c49439a23ab618727f7eb/H_vp64_r2_NT_3_1uMET1_S7_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6320ENYC/",
"accession": "IGVFFI6320ENYC",
"aliases": [
"charles-gersbach:measurement-set-crispra-control-1umET1-ipsc-cm-targeted-hicar-rep2-R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-10-23T19:29:38.328364+00:00",
"file_format": "fastq",
"file_size": 1347727028,
"href": "/sequence-files/IGVFFI6320ENYC/@@download/IGVFFI6320ENYC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/10/23/d093bfae-29d8-4823-ba04-4b8435cad778/IGVFFI6320ENYC.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0010963/",
"status": "released",
"term_name": "Illumina NextSeq 2000"
},
"status": "released",
"submitted_file_name": "/hpc/group/gersbachlab/tda17/IGVF_data_files/HiCAR/fastq/crispra_human/crispra_hicar_human_fastq/H_vp64_r2_NT_3_1uMET1_ds.93b658e4765c49439a23ab618727f7eb/H_vp64_r2_NT_3_1uMET1_S7_L001_R2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS0561MJAA/"
],
"lab": {
"@id": "/labs/charles-gersbach/",
"title": "Charles Gersbach, Duke"
},
"preferred_assay_title": "HiCAR",
"protocols": [
"https://www.protocols.io/view/hicar-for-human-ipsc-cm-following-enhancer-perturb-3byl49mdrgo5"
],
"release_timestamp": "2024-12-13T19:43:54.301405+00:00",
"samples": [
{
"@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": [
{
"@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": "26",
"status": "released",
"submitted_by": {
"@id": "/users/3782ce69-0e9f-4b46-91f9-4578139785c7/",
"title": "Ruhi Rai"
},
"submitted_files_timestamp": "2024-10-23T19:29:36.739996+00:00",
"summary": "CRISPR HiCAR integrating a non-targeting guide (sgRNA) library",
"uuid": "a3a21bd5-ea48-4d80-94ce-8c7c2ffb6ea4"
}