{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8943QPCP/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8943QPCP",
"aliases": [
"charles-gersbach:measurement-set-crispra-region3-mouse-hl1-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 [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": "Measurement set [IGVFDS8943QPCP](/measurement-sets/IGVFDS8943QPCP/) 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/IGVFDS8943QPCP/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS8943QPCP](/measurement-sets/IGVFDS8943QPCP/) has sequence file(s): [IGVFFI7660JFBM](/sequence-files/IGVFFI7660JFBM/), [IGVFFI9667BHUU](/sequence-files/IGVFFI9667BHUU/) 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/IGVFDS8943QPCP/"
}
],
"WARNING": [
{
"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/"
}
]
},
"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/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": "2024-10-23T19:20:11.295382+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"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI7660JFBM/",
"accession": "IGVFFI7660JFBM",
"aliases": [
"charles-gersbach:measurement-set-crispra-region3-mouse-hl1-targeted-hicar-rep2-R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-10-23T19:29:56.521590+00:00",
"file_format": "fastq",
"file_size": 1288622442,
"href": "/sequence-files/IGVFFI7660JFBM/@@download/IGVFFI7660JFBM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/10/23/f2e57f93-de4c-40a1-96b4-3e9e3b46279d/IGVFFI7660JFBM.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_TA446_2_noET1_ds.944e08b21dcc4f068173cb96fe66decb/HL_1_TA446_2_noET1_S15_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9667BHUU/",
"accession": "IGVFFI9667BHUU",
"aliases": [
"charles-gersbach:measurement-set-crispra-region3-mouse-hl1-targeted-hicar-rep2-R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-10-23T19:29:55.280851+00:00",
"file_format": "fastq",
"file_size": 1144641220,
"href": "/sequence-files/IGVFFI9667BHUU/@@download/IGVFFI9667BHUU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/10/23/7a2034a5-ad98-4420-93a0-157e49ec100c/IGVFFI9667BHUU.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_TA446_2_noET1_ds.944e08b21dcc4f068173cb96fe66decb/HL_1_TA446_2_noET1_S15_L001_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4066YEFI/"
],
"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": "2024-12-13T19:43:27.652383+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1004RIDZ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1004RIDZ",
"aliases": [
"charles-gersbach:in-vitro-system-crispra-region3-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"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/3782ce69-0e9f-4b46-91f9-4578139785c7/",
"title": "Ruhi Rai"
},
"submitted_files_timestamp": "2024-10-23T19:29:55.280851+00:00",
"summary": "CRISPR HiCAR integrating a guide (sgRNA) library targeting accessible genome regions in a genomic locus",
"uuid": "8cd36cce-c18e-472c-a041-03c647a77b2c"
}