{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0738WLJF/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0738WLJF",
"aliases": [
"tim-reddy:starr-seq-measurement-set-k562-P018"
],
"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 [IGVFDS0738WLJF](/measurement-sets/IGVFDS0738WLJF/) 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/IGVFDS0738WLJF/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS0738WLJF](/measurement-sets/IGVFDS0738WLJF/) has sequence file(s): [IGVFFI7758UIWT](/sequence-files/IGVFFI7758UIWT/), [IGVFFI0703ECRD](/sequence-files/IGVFFI0703ECRD/) 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/IGVFDS0738WLJF/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM5033TZAM](/in-vitro-systems/IGVFSM5033TZAM/) 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/IGVFSM5033TZAM/"
}
]
},
"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/IGVFDS5274ZJXU/",
"accession": "IGVFDS5274ZJXU",
"file_set_type": "reporter library",
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI6875LCGL/",
"accession": "IGVFFI6875LCGL",
"content_type": "variants",
"status": "released",
"summary": "GRCh38 variants"
}
],
"status": "released",
"summary": "reporter library targeting random selections genome-wide"
}
],
"control_for": [],
"creation_timestamp": "2025-02-06T03:58:27.221520+00:00",
"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/IGVFFI7758UIWT/",
"accession": "IGVFFI7758UIWT",
"aliases": [
"tim-reddy:starr-seq-rna-fastq-k562-P018-R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-02-06T04:03:36.905244+00:00",
"file_format": "fastq",
"file_size": 9307517608,
"href": "/sequence-files/IGVFFI7758UIWT/@@download/IGVFFI7758UIWT.fastq.gz",
"s3_uri": "s3://igvf-files/2025/02/06/c5edb8d3-7e55-48ef-9642-721557290d7a/IGVFFI7758UIWT.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.pool18.R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0703ECRD/",
"accession": "IGVFFI0703ECRD",
"aliases": [
"tim-reddy:starr-seq-rna-fastq-k562-P018-R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-02-06T04:03:13.036559+00:00",
"file_format": "fastq",
"file_size": 7726593885,
"href": "/sequence-files/IGVFFI0703ECRD/@@download/IGVFFI0703ECRD.fastq.gz",
"s3_uri": "s3://igvf-files/2025/02/06/97e71100-7eda-40fb-8b28-7b959b773d50/IGVFFI0703ECRD.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.pool18.R1.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS8554TSTG/"
],
"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": "2025-04-09T16:39:59.251867+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5033TZAM/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5033TZAM",
"aliases": [
"tim-reddy:starr-seq-k562-P018"
],
"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": "2025-02-06T04:03:13.036559+00:00",
"summary": "SUPERSTARR integrating a reporter library targeting random selections genome-wide",
"uuid": "a63f7ba3-b826-4f65-b148-4407201a3c92"
}