{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2472COJU/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2472COJU",
"aliases": [
"charles-gersbach:measurement-set-crispri-region3-ipsc-cm-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 [IGVFDS2472COJU](/measurement-sets/IGVFDS2472COJU/) has sequence file(s): [IGVFFI1819WFUE](/sequence-files/IGVFFI1819WFUE/), [IGVFFI6329SYEP](/sequence-files/IGVFFI6329SYEP/) 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/IGVFDS2472COJU/"
}
]
},
"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": "2024-10-23T19:19:54.755693+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO3212TBUN/",
"accession": "IGVFDO3212TBUN",
"aliases": [
"charles-gersbach:human-donor-WTC11"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI1819WFUE/",
"accession": "IGVFFI1819WFUE",
"aliases": [
"charles-gersbach:measurement-set-crispri-region3-ipsc-cm-targeted-hicar-rep1-R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-10-23T19:29:14.795428+00:00",
"file_format": "fastq",
"file_size": 2100582295,
"href": "/sequence-files/IGVFFI1819WFUE/@@download/IGVFFI1819WFUE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/10/23/b5192e9d-966a-44a9-bdfe-04770d32a83a/IGVFFI1819WFUE.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/crispri/crispri_hicar_fastq/probe_enriched_krab_region3_1_L1_ds.e7a6b7f561604ed5af818e77e969c199/probe_enriched_krab_region3_1_S5_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6329SYEP/",
"accession": "IGVFFI6329SYEP",
"aliases": [
"charles-gersbach:measurement-set-crispri-region3-ipsc-cm-targeted-hicar-rep1-R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-10-23T19:29:15.902462+00:00",
"file_format": "fastq",
"file_size": 2360059612,
"href": "/sequence-files/IGVFFI6329SYEP/@@download/IGVFFI6329SYEP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/10/23/aad9a6ef-f5ed-4b31-82e6-8390ebfe6da1/IGVFFI6329SYEP.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/crispri/crispri_hicar_fastq/probe_enriched_krab_region3_1_L1_ds.e7a6b7f561604ed5af818e77e969c199/probe_enriched_krab_region3_1_S5_L001_R2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS7841JHCX/"
],
"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": "2024-12-13T19:43:33.076310+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5947VCGI/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5947VCGI",
"aliases": [
"charles-gersbach:in-vitro-system-crispri-region3-ipsc-cm-targeted-hicar-rep1"
],
"classifications": [
"differentiated cell specimen"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS2023ZEFC/",
"accession": "IGVFDS2023ZEFC",
"file_set_type": "guide library",
"status": "released",
"summary": "guide (sgRNA) library targeting accessible genome regions in a genomic locus"
}
],
"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": "GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 42 days, male, Homo sapiens 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": "23",
"status": "released",
"submitted_by": {
"@id": "/users/3782ce69-0e9f-4b46-91f9-4578139785c7/",
"title": "Ruhi Rai"
},
"submitted_files_timestamp": "2024-10-23T19:29:14.795428+00:00",
"summary": "CRISPR HiCAR integrating a guide (sgRNA) library targeting accessible genome regions in a genomic locus",
"uuid": "e522313e-daba-431a-96f4-3d2b46eab30f"
}