{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3127UNFB/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3127UNFB",
"aliases": [
"charles-gersbach:measurement-set-crispra-region3-1umET1-ipsc-cm-targeted-hicar-rep2"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002440/",
"status": "released",
"term_name": "Hi-C assay"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS3127UNFB](/measurement-sets/IGVFDS3127UNFB/) has sequence file(s): [IGVFFI7905CWZC](/sequence-files/IGVFFI7905CWZC/), [IGVFFI4866TRQV](/sequence-files/IGVFFI4866TRQV/) 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/IGVFDS3127UNFB/"
}
]
},
"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": "2024-10-23T19:20:06.057565+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/IGVFFI7905CWZC/",
"accession": "IGVFFI7905CWZC",
"aliases": [
"charles-gersbach:measurement-set-crispra-region3-1umET1-ipsc-cm-targeted-hicar-rep2-R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-10-23T19:29:41.467192+00:00",
"file_format": "fastq",
"file_size": 875274832,
"href": "/sequence-files/IGVFFI7905CWZC/@@download/IGVFFI7905CWZC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/10/23/b0ecf54e-b6dd-4c0e-a82c-105a0c8bec0f/IGVFFI7905CWZC.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_TA448_2_1uMET1_ds.2cb990959235460a9894f1a50e0bbfdb/H_vp64_r2_TA448_2_1uMET1_S9_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4866TRQV/",
"accession": "IGVFFI4866TRQV",
"aliases": [
"charles-gersbach:measurement-set-crispra-region3-1umET1-ipsc-cm-targeted-hicar-rep2-R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-10-23T19:29:42.613168+00:00",
"file_format": "fastq",
"file_size": 974160109,
"href": "/sequence-files/IGVFFI4866TRQV/@@download/IGVFFI4866TRQV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/10/23/0c81e677-2a41-4942-9d72-603bfff54322/IGVFFI4866TRQV.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_TA448_2_1uMET1_ds.2cb990959235460a9894f1a50e0bbfdb/H_vp64_r2_TA448_2_1uMET1_S9_L001_R2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS2296EFNK/"
],
"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": "2024-12-13T19:43:52.150872+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1839OFIJ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1839OFIJ",
"aliases": [
"charles-gersbach:in-vitro-system-crispra-region3-1umET1-ipsc-cm-targeted-hicar-rep2"
],
"classifications": [
"differentiated cell specimen"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS5972DQKC/",
"accession": "IGVFDS5972DQKC",
"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 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/",
"status": "released",
"treatment_term_name": "Endothelin-1"
}
]
}
],
"schema_version": "23",
"status": "released",
"submitted_by": {
"@id": "/users/3782ce69-0e9f-4b46-91f9-4578139785c7/",
"title": "Ruhi Rai"
},
"submitted_files_timestamp": "2024-10-23T19:29:41.467192+00:00",
"summary": "CRISPR HiCAR integrating a guide (sgRNA) library targeting accessible genome regions in a genomic locus",
"uuid": "5c33800c-df55-4a8c-9dd2-e3b89e30c179"
}