{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS1147GIJW/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1147GIJW",
"aliases": [
"tim-reddy:starr-seq-principal-analysis-set-k562-P015"
],
"assay_titles": [
"SUPERSTARR"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "Analysis set [IGVFDS1147GIJW](/analysis-sets/IGVFDS1147GIJW/) 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": "/analysis-sets/IGVFDS1147GIJW/"
},
{
"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/"
}
]
},
"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": "2025-02-06T04:00:44.478124+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO9208RPQQ/",
"accession": "IGVFDO9208RPQQ",
"aliases": [
"igvf:donor_of_K562"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "principal analysis",
"files": [
{
"@id": "/alignment-files/IGVFFI3281LZFI/",
"accession": "IGVFFI3281LZFI",
"aliases": [
"tim-reddy:starr-seq-dna-bam-k562-P015"
],
"assembly": "GRCh38",
"content_type": "alignments",
"controlled_access": false,
"creation_timestamp": "2025-02-06T14:26:54.321544+00:00",
"file_format": "bam",
"file_size": 7248410583,
"href": "/alignment-files/IGVFFI3281LZFI/@@download/IGVFFI3281LZFI.bam",
"s3_uri": "s3://igvf-files/2025/02/06/d481c846-37d8-474d-807a-d58ffa788017/IGVFFI3281LZFI.bam",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_1_STARR_seq/K562.starrseq.dna.pool15.f3q10.sorted.dups_marked.bam",
"upload_status": "validated"
},
{
"@id": "/alignment-files/IGVFFI9281CXZP/",
"accession": "IGVFFI9281CXZP",
"aliases": [
"tim-reddy:starr-seq-rna-bam-k562-P015"
],
"assembly": "GRCh38",
"content_type": "alignments",
"controlled_access": false,
"creation_timestamp": "2025-02-06T14:27:18.577878+00:00",
"file_format": "bam",
"file_size": 8751559140,
"href": "/alignment-files/IGVFFI9281CXZP/@@download/IGVFFI9281CXZP.bam",
"s3_uri": "s3://igvf-files/2025/02/06/c7008f8c-6bdf-46ac-9f1f-598b3d7e8c86/IGVFFI9281CXZP.bam",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_1_STARR_seq/K562.starrseq.rna.pool15.f3q10.sorted.with_umis.dups_marked.bam",
"upload_status": "validated"
},
{
"@id": "/index-files/IGVFFI0618ONQE/",
"accession": "IGVFFI0618ONQE",
"aliases": [
"tim-reddy:starr-seq-dna-bam-bai-k562-P015"
],
"assembly": "GRCh38",
"content_type": "index",
"creation_timestamp": "2025-02-06T15:45:02.296159+00:00",
"file_format": "bai",
"file_size": 2432960,
"href": "/index-files/IGVFFI0618ONQE/@@download/IGVFFI0618ONQE.bai",
"s3_uri": "s3://igvf-files/2025/02/06/83dd0b25-bacd-4f7f-a784-e0f035c37cdd/IGVFFI0618ONQE.bai",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_1_STARR_seq/K562.starrseq.dna.pool15.f3q10.sorted.dups_marked.bam.bai",
"upload_status": "validated"
},
{
"@id": "/index-files/IGVFFI3069EYZK/",
"accession": "IGVFFI3069EYZK",
"aliases": [
"tim-reddy:starr-seq-rna-bam-bai-k562-P015"
],
"assembly": "GRCh38",
"content_type": "index",
"creation_timestamp": "2025-02-06T15:45:24.281367+00:00",
"file_format": "bai",
"file_size": 2834552,
"href": "/index-files/IGVFFI3069EYZK/@@download/IGVFFI3069EYZK.bai",
"s3_uri": "s3://igvf-files/2025/02/06/36bb2f53-7f61-458a-800d-13d60f58e478/IGVFFI3069EYZK.bai",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_1_STARR_seq/K562.starrseq.rna.pool15.f3q10.sorted.with_umis.dups_marked.bam.bai",
"upload_status": "validated"
},
{
"@id": "/alignment-files/IGVFFI0792RKNX/",
"accession": "IGVFFI0792RKNX",
"aliases": [
"tim-reddy:starr-seq-rna-bam-personal-genome-P015"
],
"assembly": "custom",
"content_type": "alignments",
"controlled_access": false,
"creation_timestamp": "2025-02-06T16:25:53.799958+00:00",
"file_format": "bam",
"file_size": 8915768640,
"href": "/alignment-files/IGVFFI0792RKNX/@@download/IGVFFI0792RKNX.bam",
"s3_uri": "s3://igvf-files/2025/02/06/1a6aaa08-f7fa-44de-8764-340de918e6d2/IGVFFI0792RKNX.bam",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_1_STARR_seq/K562.starrseq.rna.pool15.personal_genome.sorted.bam",
"upload_status": "validated"
},
{
"@id": "/alignment-files/IGVFFI2664SVPC/",
"accession": "IGVFFI2664SVPC",
"aliases": [
"tim-reddy:starr-seq-dna-bam-personal-genome-P015"
],
"assembly": "custom",
"content_type": "alignments",
"controlled_access": false,
"creation_timestamp": "2025-02-06T16:25:32.312231+00:00",
"file_format": "bam",
"file_size": 7530027814,
"href": "/alignment-files/IGVFFI2664SVPC/@@download/IGVFFI2664SVPC.bam",
"s3_uri": "s3://igvf-files/2025/02/06/a815a68b-c8d3-4bbf-b442-d174a3754870/IGVFFI2664SVPC.bam",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_1_STARR_seq/K562.starrseq.dna.pool15.personal_genome.sorted.bam",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI6848AZTR/",
"accession": "IGVFFI6848AZTR",
"aliases": [
"tim-reddy:starr-seq-bird-input-file-P015"
],
"assembly": "GRCh38",
"content_type": "reporter variants",
"controlled_access": false,
"creation_timestamp": "2025-02-07T15:58:30.652731+00:00",
"file_format": "tsv",
"file_size": 31087655,
"href": "/tabular-files/IGVFFI6848AZTR/@@download/IGVFFI6848AZTR.tsv.gz",
"s3_uri": "s3://igvf-files/2025/02/07/292db57a-6d8d-48df-904b-d5fc435fac34/IGVFFI6848AZTR.tsv.gz",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_1_STARR_seq/K562.starrseq.bird_input.spdi.pool15.txt.gz",
"upload_status": "validation exempted"
},
{
"@id": "/tabular-files/IGVFFI2419QNNR/",
"accession": "IGVFFI2419QNNR",
"aliases": [
"tim-reddy:starr-seq-bird-output-file-P015"
],
"assembly": "GRCh38",
"content_type": "reporter genomic variant effects",
"controlled_access": false,
"creation_timestamp": "2025-02-07T17:22:49.814214+00:00",
"file_format": "tsv",
"file_size": 75078518,
"href": "/tabular-files/IGVFFI2419QNNR/@@download/IGVFFI2419QNNR.tsv.gz",
"s3_uri": "s3://igvf-files/2025/02/07/ddc57c96-566c-4e69-9c7d-2cb6c54a9db6/IGVFFI2419QNNR.tsv.gz",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_1_STARR_seq/K562.starrseq.bird_output.spdi.pool15.txt.gz",
"upload_status": "validated"
},
{
"@id": "/index-files/IGVFFI6237APJK/",
"accession": "IGVFFI6237APJK",
"aliases": [
"tim-reddy:starr-seq-dna-bam-bai-personal-genome-P015"
],
"assembly": "custom",
"content_type": "index",
"creation_timestamp": "2025-02-10T18:23:45.384199+00:00",
"file_format": "bai",
"file_size": 2459160,
"href": "/index-files/IGVFFI6237APJK/@@download/IGVFFI6237APJK.bai",
"s3_uri": "s3://igvf-files/2025/02/10/1f721e19-f2e5-417f-bed4-cabdeedb80ac/IGVFFI6237APJK.bai",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_1_STARR_seq/K562.starrseq.dna.pool15.personal_genome.sorted.bam.bai",
"upload_status": "validated"
},
{
"@id": "/index-files/IGVFFI4825OFOD/",
"accession": "IGVFFI4825OFOD",
"aliases": [
"tim-reddy:starr-seq-rna-bam-bai-personal-genome-P015"
],
"assembly": "custom",
"content_type": "index",
"creation_timestamp": "2025-02-10T18:24:10.207069+00:00",
"file_format": "bai",
"file_size": 2819960,
"href": "/index-files/IGVFFI4825OFOD/@@download/IGVFFI4825OFOD.bai",
"s3_uri": "s3://igvf-files/2025/02/10/204d78ff-cc51-408e-98d1-39cebe16822b/IGVFFI4825OFOD.bai",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_1_STARR_seq/K562.starrseq.rna.pool15.personal_genome.sorted.bam.bai",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI3017XGQB/",
"accession": "IGVFFI3017XGQB",
"aliases": [
"tim-reddy:starr-seq-bird-reporter-variant-file-P015"
],
"assembly": "GRCh38",
"content_type": "reporter genomic variant effects",
"controlled_access": false,
"creation_timestamp": "2025-03-13T21:13:11.622016+00:00",
"file_format": "tsv",
"file_size": 162488032,
"href": "/tabular-files/IGVFFI3017XGQB/@@download/IGVFFI3017XGQB.tsv.gz",
"s3_uri": "s3://igvf-files/2025/03/13/53fb5e15-6618-442d-8faa-efcb0f491715/IGVFFI3017XGQB.tsv.gz",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_1_STARR_seq/K562.starrseq.bird_reporter_variant.pool15.na_empty.txt.gz",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/measurement-sets/IGVFDS9299BLCE/",
"accession": "IGVFDS9299BLCE",
"aliases": [
"tim-reddy:starr-seq-measurement-set-k562-P015"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/construct-library-sets/IGVFDS5042GGCM/",
"accession": "IGVFDS5042GGCM",
"aliases": [
"tim-reddy:starr-seq-construct-lib-P015"
],
"file_set_type": "reporter library",
"status": "released"
}
],
"input_for": [],
"lab": {
"@id": "/labs/tim-reddy/",
"title": "Tim Reddy, Duke"
},
"protocols": [
"https://www.protocols.io/view/whole-genome-starr-seq-protocol-reddy-lab-d6ct9awn"
],
"release_timestamp": "2025-04-09T16:40:11.543043+00:00",
"sample_summary": "Homo sapiens K562 cell line, transfected with a reporter library",
"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": "9",
"status": "released",
"submitted_by": {
"@id": "/users/29f5f78d-ac90-421e-90c6-a90e1dc407a7/",
"title": "Alejandro Barrera"
},
"submitted_files_timestamp": "2025-02-06T14:26:54.321544+00:00",
"summary": "SUPERSTARR: alignments, index, reporter genomic variant effects, reporter variants",
"uuid": "611128fe-3bf5-4dab-acd0-c0c4becd0336",
"workflows": [
{
"@id": "/workflows/IGVFWF6957ZNII/",
"accession": "IGVFWF6957ZNII",
"name": "SUPERSTARR Pipeline",
"status": "in progress",
"uniform_pipeline": false
}
]
}