{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1089VHTM/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1089VHTM",
"aliases": [
"charles-gersbach:measurement-set-crispra-control-mouse-hl1-targeted-hicar-rep1"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002440/",
"status": "released",
"term_name": "Hi-C assay"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS1089VHTM](/measurement-sets/IGVFDS1089VHTM/) has sequence file(s): [IGVFFI1445GVNW](/sequence-files/IGVFFI1445GVNW/), [IGVFFI9080GXFN](/sequence-files/IGVFFI9080GXFN/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS1089VHTM/"
}
]
},
"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"
},
"control_for": [],
"creation_timestamp": "2024-10-23T19:20:07.762790+00:00",
"donors": [
{
"@id": "/rodent-donors/IGVFDO1434JYIN/",
"accession": "IGVFDO1434JYIN",
"aliases": [
"charles-gersbach:mouse-donor-HL-1"
],
"sex": "female",
"status": "released",
"taxa": "Mus musculus"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI1445GVNW/",
"accession": "IGVFFI1445GVNW",
"aliases": [
"charles-gersbach:measurement-set-crispra-control-mouse-hl1-targeted-hicar-rep1-R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-10-23T19:29:47.180783+00:00",
"file_format": "fastq",
"file_size": 1325705691,
"href": "/sequence-files/IGVFFI1445GVNW/@@download/IGVFFI1445GVNW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/10/23/d75d7e65-b741-4be9-a6a4-a710112e9f92/IGVFFI1445GVNW.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_mouse/crispra_hicar_mouse_fastq/HL_1_TA432_NT_1_noET1_ds.cf4cef3a109a4e3da737a08d710b3099/HL_1_TA432_NT_1_noET1_S11_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9080GXFN/",
"accession": "IGVFFI9080GXFN",
"aliases": [
"charles-gersbach:measurement-set-crispra-control-mouse-hl1-targeted-hicar-rep1-R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-10-23T19:29:46.029512+00:00",
"file_format": "fastq",
"file_size": 1191873943,
"href": "/sequence-files/IGVFFI9080GXFN/@@download/IGVFFI9080GXFN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/10/23/890f76d1-304e-4ab9-93c5-3a1baeb64e66/IGVFFI9080GXFN.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_mouse/crispra_hicar_mouse_fastq/HL_1_TA432_NT_1_noET1_ds.cf4cef3a109a4e3da737a08d710b3099/HL_1_TA432_NT_1_noET1_S11_L001_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS0318CFLU/"
],
"lab": {
"@id": "/labs/charles-gersbach/",
"title": "Charles Gersbach, Duke"
},
"preferred_assay_title": "HiCAR",
"protocols": [
"https://www.protocols.io/view/hicar-for-mouse-hl-1-cells-following-enhancer-pert-36wgqn2yygk5"
],
"release_timestamp": "2024-12-13T19:43:28.170856+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM6964SBRF/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6964SBRF",
"aliases": [
"charles-gersbach:in-vitro-system-crispra-control-mouse-hl1-targeted-hicar-rep1"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS4536EZHP/",
"accession": "IGVFDS4536EZHP",
"file_set_type": "guide library",
"status": "released",
"summary": "non-targeting guide (sgRNA) library"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0022835/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "HL-1",
"term_name": "HL-1"
}
],
"status": "released",
"summary": "HL-1 cell line, female, Mus musculus C57BL/6J transfected with a guide library",
"taxa": "Mus musculus"
}
],
"schema_version": "23",
"status": "released",
"submitted_by": {
"@id": "/users/3782ce69-0e9f-4b46-91f9-4578139785c7/",
"title": "Ruhi Rai"
},
"submitted_files_timestamp": "2024-10-23T19:29:46.029512+00:00",
"summary": "CRISPR HiCAR integrating a non-targeting guide (sgRNA) library",
"uuid": "9a6aa455-3170-4be0-9f8a-edbd34e8a1c3"
}