{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8619XCTL/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8619XCTL",
"aliases": [
"tim-reddy:starr-seq-measurement-set-k562-P012"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002041/",
"assay_slims": [
"reporter"
],
"status": "released",
"term_name": "self-transcribing active regulatory region sequencing assay"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS8619XCTL](/measurement-sets/IGVFDS8619XCTL/) 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/IGVFDS8619XCTL/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS8619XCTL](/measurement-sets/IGVFDS8619XCTL/) has sequence file(s): [IGVFFI6158KSWI](/sequence-files/IGVFFI6158KSWI/), [IGVFFI2862JXUN](/sequence-files/IGVFFI2862JXUN/) 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/IGVFDS8619XCTL/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM1399HFHX](/in-vitro-systems/IGVFSM1399HFHX/) 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/IGVFSM1399HFHX/"
}
]
},
"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/IGVFDS0228CLFT/",
"accession": "IGVFDS0228CLFT",
"file_set_type": "reporter library",
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI5876KVON/",
"accession": "IGVFFI5876KVON",
"content_type": "variants",
"status": "released",
"summary": "GRCh38 variants"
}
],
"status": "released",
"summary": "reporter library targeting random selections genome-wide"
}
],
"control_for": [],
"creation_timestamp": "2025-02-06T03:58:20.510801+00:00",
"data_use_limitation_summaries": [
"no certificate"
],
"donors": [
{
"@id": "/human-donors/IGVFDO9208RPQQ/",
"accession": "IGVFDO9208RPQQ",
"aliases": [
"igvf:donor_of_K562"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI6158KSWI/",
"accession": "IGVFFI6158KSWI",
"aliases": [
"tim-reddy:starr-seq-rna-fastq-k562-P012-R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-02-06T04:03:03.357573+00:00",
"file_format": "fastq",
"file_size": 9650092254,
"href": "/sequence-files/IGVFFI6158KSWI/@@download/IGVFFI6158KSWI.fastq.gz",
"md5sum": "f0865e245dce0c3f76a5f0c72e2b0c57",
"s3_uri": "s3://igvf-files/2025/02/06/2e240c2c-2207-4c94-861c-858d73ddb348/IGVFFI6158KSWI.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0010963/",
"status": "released",
"term_name": "Illumina NextSeq 2000"
},
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/raw_data/AIM_1_STARR_seq/K562.starrseq.rna.pool12.R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2862JXUN/",
"accession": "IGVFFI2862JXUN",
"aliases": [
"tim-reddy:starr-seq-rna-fastq-k562-P012-R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-02-06T04:03:27.080040+00:00",
"file_format": "fastq",
"file_size": 11779628943,
"href": "/sequence-files/IGVFFI2862JXUN/@@download/IGVFFI2862JXUN.fastq.gz",
"md5sum": "7cead32c8b48a5367b32ef6433ce1e35",
"s3_uri": "s3://igvf-files/2025/02/06/d90a6a34-079a-491a-bac2-77bc8c545f02/IGVFFI2862JXUN.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0010963/",
"status": "released",
"term_name": "Illumina NextSeq 2000"
},
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/raw_data/AIM_1_STARR_seq/K562.starrseq.rna.pool12.R2.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS9219WLAH/"
],
"lab": {
"@id": "/labs/tim-reddy/",
"title": "Tim Reddy, Duke"
},
"preferred_assay_title": "SUPERSTARR",
"protocols": [
"https://www.protocols.io/view/whole-genome-starr-seq-protocol-reddy-lab-d6ct9awn"
],
"release_timestamp": "2025-04-09T16:40:02.278483+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1399HFHX/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1399HFHX",
"aliases": [
"tim-reddy:starr-seq-k562-P012"
],
"classifications": [
"cell line"
],
"institutional_certificates": [],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002067/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:K562"
],
"status": "released",
"summary": "K562",
"term_name": "K562"
}
],
"status": "released",
"summary": "Homo sapiens (female) K562 cell line transfected with a reporter library",
"taxa": "Homo sapiens"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/29f5f78d-ac90-421e-90c6-a90e1dc407a7/",
"title": "Alejandro Barrera"
},
"submitted_files_timestamp": "2025-02-06T04:03:03.357573+00:00",
"summary": "SUPERSTARR integrating a reporter library targeting random selections genome-wide",
"uuid": "822270c2-2012-4a25-9522-6be14a6d2681"
}