{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9299BLCE/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9299BLCE",
"aliases": [
"tim-reddy:starr-seq-measurement-set-k562-P015"
],
"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": "In vitro system [IGVFSM4814FXFA](/in-vitro-systems/IGVFSM4814FXFA/) 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/IGVFSM4814FXFA/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS9299BLCE](/measurement-sets/IGVFDS9299BLCE/) 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/IGVFDS9299BLCE/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS9299BLCE](/measurement-sets/IGVFDS9299BLCE/) has sequence file(s): [IGVFFI7315ZVTL](/sequence-files/IGVFFI7315ZVTL/), [IGVFFI5627JVSD](/sequence-files/IGVFFI5627JVSD/) 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/IGVFDS9299BLCE/"
}
]
},
"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/IGVFDS5042GGCM/",
"accession": "IGVFDS5042GGCM",
"file_set_type": "reporter library",
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI5520HIUN/",
"accession": "IGVFFI5520HIUN",
"content_type": "variants",
"status": "released",
"summary": "GRCh38 variants"
}
],
"status": "released",
"summary": "reporter library targeting random selections genome-wide"
}
],
"control_for": [],
"creation_timestamp": "2025-02-06T03:58:24.574477+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/IGVFFI7315ZVTL/",
"accession": "IGVFFI7315ZVTL",
"aliases": [
"tim-reddy:starr-seq-rna-fastq-k562-P015-R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-02-06T04:03:08.465391+00:00",
"file_format": "fastq",
"file_size": 8686837823,
"href": "/sequence-files/IGVFFI7315ZVTL/@@download/IGVFFI7315ZVTL.fastq.gz",
"md5sum": "77a43049fd2b24833b1482b5074e5a75",
"s3_uri": "s3://igvf-files/2025/02/06/4989b5f8-1f5e-47f9-a054-b99f5cde2e70/IGVFFI7315ZVTL.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.pool15.R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5627JVSD/",
"accession": "IGVFFI5627JVSD",
"aliases": [
"tim-reddy:starr-seq-rna-fastq-k562-P015-R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-02-06T04:03:31.639571+00:00",
"file_format": "fastq",
"file_size": 10347681013,
"href": "/sequence-files/IGVFFI5627JVSD/@@download/IGVFFI5627JVSD.fastq.gz",
"md5sum": "4054b3c43da26b94c052578c232d726c",
"s3_uri": "s3://igvf-files/2025/02/06/98fdc3a8-bd4b-442b-96df-44427f7f7a88/IGVFFI5627JVSD.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.pool15.R2.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS1147GIJW/"
],
"lab": {
"@id": "/labs/tim-reddy/",
"title": "Tim Reddy, Duke"
},
"preferred_assay_title": "STARR-seq",
"protocols": [
"https://www.protocols.io/view/whole-genome-starr-seq-protocol-reddy-lab-d6ct9awn"
],
"release_timestamp": "2025-04-09T16:40:11.996628+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4814FXFA/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4814FXFA",
"aliases": [
"tim-reddy:starr-seq-k562-P015"
],
"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": "2025-02-06T04:03:08.465391+00:00",
"summary": "STARR-seq integrating a reporter library targeting random selections genome-wide",
"uuid": "961ba9b9-216a-44ce-ac11-70a4fbde2239"
}