{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS6219XNKZ/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6219XNKZ",
"aliases": [
"tim-reddy:starr-seq-principal-analysis-set-k562-P016"
],
"assay_titles": [
"SUPERSTARR"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM8103VLQU](/in-vitro-systems/IGVFSM8103VLQU/) 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/IGVFSM8103VLQU/"
},
{
"category": "missing publication",
"detail": "Analysis set [IGVFDS6219XNKZ](/analysis-sets/IGVFDS6219XNKZ/) 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/IGVFDS6219XNKZ/"
}
]
},
"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/IGVFDS1243NBLH/",
"accession": "IGVFDS1243NBLH",
"file_set_type": "reporter library",
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI5966HEII/",
"accession": "IGVFFI5966HEII",
"content_type": "variants",
"status": "released",
"summary": "GRCh38 variants"
}
],
"status": "released",
"summary": "reporter library targeting random selections genome-wide"
}
],
"control_for": [],
"creation_timestamp": "2025-02-06T04:00:45.397973+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": "/index-files/IGVFFI6176CRVD/",
"accession": "IGVFFI6176CRVD",
"aliases": [
"tim-reddy:starr-seq-dna-bam-bai-k562-P016"
],
"assembly": "GRCh38",
"content_type": "index",
"creation_timestamp": "2025-02-06T15:45:03.511889+00:00",
"file_format": "bai",
"file_size": 2818504,
"href": "/index-files/IGVFFI6176CRVD/@@download/IGVFFI6176CRVD.bai",
"s3_uri": "s3://igvf-files/2025/02/06/207d29be-35dd-4b6a-8b05-64534c850d65/IGVFFI6176CRVD.bai",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_1_STARR_seq/K562.starrseq.dna.pool16.f3q10.sorted.dups_marked.bam.bai",
"upload_status": "validated"
},
{
"@id": "/index-files/IGVFFI1092EISH/",
"accession": "IGVFFI1092EISH",
"aliases": [
"tim-reddy:starr-seq-rna-bam-bai-k562-P016"
],
"assembly": "GRCh38",
"content_type": "index",
"creation_timestamp": "2025-02-06T15:45:25.552439+00:00",
"file_format": "bai",
"file_size": 3419176,
"href": "/index-files/IGVFFI1092EISH/@@download/IGVFFI1092EISH.bai",
"s3_uri": "s3://igvf-files/2025/02/06/9924c16c-6b38-4e0a-8f7d-96cc2ab425c3/IGVFFI1092EISH.bai",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_1_STARR_seq/K562.starrseq.rna.pool16.f3q10.sorted.with_umis.dups_marked.bam.bai",
"upload_status": "validated"
},
{
"@id": "/alignment-files/IGVFFI5206MZCI/",
"accession": "IGVFFI5206MZCI",
"aliases": [
"tim-reddy:starr-seq-dna-bam-k562-P016"
],
"assembly": "GRCh38",
"content_type": "alignments",
"controlled_access": false,
"creation_timestamp": "2025-02-06T14:26:55.813707+00:00",
"file_format": "bam",
"file_size": 6611076309,
"href": "/alignment-files/IGVFFI5206MZCI/@@download/IGVFFI5206MZCI.bam",
"s3_uri": "s3://igvf-files/2025/02/06/d0dd4ea4-02d1-45e3-871e-c088410d727b/IGVFFI5206MZCI.bam",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_1_STARR_seq/K562.starrseq.dna.pool16.f3q10.sorted.dups_marked.bam",
"upload_status": "validated"
},
{
"@id": "/alignment-files/IGVFFI7067LDJI/",
"accession": "IGVFFI7067LDJI",
"aliases": [
"tim-reddy:starr-seq-rna-bam-k562-P016"
],
"assembly": "GRCh38",
"content_type": "alignments",
"controlled_access": false,
"creation_timestamp": "2025-02-06T14:27:20.606443+00:00",
"file_format": "bam",
"file_size": 9893894261,
"href": "/alignment-files/IGVFFI7067LDJI/@@download/IGVFFI7067LDJI.bam",
"s3_uri": "s3://igvf-files/2025/02/06/f7011881-9e7e-4297-99e2-7bafc4c44ded/IGVFFI7067LDJI.bam",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_1_STARR_seq/K562.starrseq.rna.pool16.f3q10.sorted.with_umis.dups_marked.bam",
"upload_status": "validated"
},
{
"@id": "/alignment-files/IGVFFI7427DHSR/",
"accession": "IGVFFI7427DHSR",
"aliases": [
"tim-reddy:starr-seq-rna-bam-personal-genome-P016"
],
"assembly": "custom",
"content_type": "alignments",
"controlled_access": false,
"creation_timestamp": "2025-02-06T16:25:55.143726+00:00",
"file_format": "bam",
"file_size": 9982963467,
"href": "/alignment-files/IGVFFI7427DHSR/@@download/IGVFFI7427DHSR.bam",
"s3_uri": "s3://igvf-files/2025/02/06/6d339043-3669-48f2-9ae0-c77c0001f176/IGVFFI7427DHSR.bam",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_1_STARR_seq/K562.starrseq.rna.pool16.personal_genome.sorted.bam",
"upload_status": "validated"
},
{
"@id": "/alignment-files/IGVFFI5820VTXJ/",
"accession": "IGVFFI5820VTXJ",
"aliases": [
"tim-reddy:starr-seq-dna-bam-personal-genome-P016"
],
"assembly": "custom",
"content_type": "alignments",
"controlled_access": false,
"creation_timestamp": "2025-02-06T16:25:33.671292+00:00",
"file_format": "bam",
"file_size": 6859254440,
"href": "/alignment-files/IGVFFI5820VTXJ/@@download/IGVFFI5820VTXJ.bam",
"s3_uri": "s3://igvf-files/2025/02/06/3a944314-2d0f-452c-8900-b17cf71d9d7d/IGVFFI5820VTXJ.bam",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_1_STARR_seq/K562.starrseq.dna.pool16.personal_genome.sorted.bam",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI4661JKOA/",
"accession": "IGVFFI4661JKOA",
"aliases": [
"tim-reddy:starr-seq-bird-input-file-P016"
],
"assembly": "GRCh38",
"content_type": "reporter variants",
"controlled_access": false,
"creation_timestamp": "2025-02-07T15:58:32.015538+00:00",
"file_format": "tsv",
"file_size": 19604106,
"href": "/tabular-files/IGVFFI4661JKOA/@@download/IGVFFI4661JKOA.tsv.gz",
"s3_uri": "s3://igvf-files/2025/02/07/7a6004d8-b07b-41f0-9e66-4a46ce2965a3/IGVFFI4661JKOA.tsv.gz",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_1_STARR_seq/K562.starrseq.bird_input.spdi.pool16.txt.gz",
"upload_status": "validation exempted"
},
{
"@id": "/tabular-files/IGVFFI3120NHVD/",
"accession": "IGVFFI3120NHVD",
"aliases": [
"tim-reddy:starr-seq-bird-output-file-P016"
],
"assembly": "GRCh38",
"content_type": "reporter genomic variant effects",
"controlled_access": false,
"creation_timestamp": "2025-02-07T17:22:51.547143+00:00",
"file_format": "tsv",
"file_size": 46706570,
"href": "/tabular-files/IGVFFI3120NHVD/@@download/IGVFFI3120NHVD.tsv.gz",
"s3_uri": "s3://igvf-files/2025/02/07/f2e59758-812a-43ff-a4b7-ab20dbf25126/IGVFFI3120NHVD.tsv.gz",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_1_STARR_seq/K562.starrseq.bird_output.spdi.pool16.txt.gz",
"upload_status": "validated"
},
{
"@id": "/index-files/IGVFFI5967DXJI/",
"accession": "IGVFFI5967DXJI",
"aliases": [
"tim-reddy:starr-seq-dna-bam-bai-personal-genome-P016"
],
"assembly": "custom",
"content_type": "index",
"creation_timestamp": "2025-02-10T18:23:47.464876+00:00",
"file_format": "bai",
"file_size": 2822816,
"href": "/index-files/IGVFFI5967DXJI/@@download/IGVFFI5967DXJI.bai",
"s3_uri": "s3://igvf-files/2025/02/10/6e195ea7-e183-4d13-b4e9-6ca0eeffa527/IGVFFI5967DXJI.bai",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_1_STARR_seq/K562.starrseq.dna.pool16.personal_genome.sorted.bam.bai",
"upload_status": "validated"
},
{
"@id": "/index-files/IGVFFI2714HBMR/",
"accession": "IGVFFI2714HBMR",
"aliases": [
"tim-reddy:starr-seq-rna-bam-bai-personal-genome-P016"
],
"assembly": "custom",
"content_type": "index",
"creation_timestamp": "2025-02-10T18:24:11.585056+00:00",
"file_format": "bai",
"file_size": 3375504,
"href": "/index-files/IGVFFI2714HBMR/@@download/IGVFFI2714HBMR.bai",
"s3_uri": "s3://igvf-files/2025/02/10/d2aa3c51-4de9-46a5-bcc0-582975d5935b/IGVFFI2714HBMR.bai",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_1_STARR_seq/K562.starrseq.rna.pool16.personal_genome.sorted.bam.bai",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI5113EDFC/",
"accession": "IGVFFI5113EDFC",
"aliases": [
"tim-reddy:starr-seq-bird-reporter-variant-file-P016"
],
"assembly": "GRCh38",
"content_type": "reporter genomic variant effects",
"controlled_access": false,
"creation_timestamp": "2025-03-13T21:13:13.184682+00:00",
"file_format": "tsv",
"file_size": 102401195,
"href": "/tabular-files/IGVFFI5113EDFC/@@download/IGVFFI5113EDFC.tsv.gz",
"s3_uri": "s3://igvf-files/2025/03/13/258db3db-e1bd-48b1-bfef-dcbf20027a95/IGVFFI5113EDFC.tsv.gz",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_1_STARR_seq/K562.starrseq.bird_reporter_variant.pool16.na_empty.txt.gz",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/measurement-sets/IGVFDS9547KOMP/",
"accession": "IGVFDS9547KOMP",
"aliases": [
"tim-reddy:starr-seq-measurement-set-k562-P016"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/construct-library-sets/IGVFDS1243NBLH/",
"accession": "IGVFDS1243NBLH",
"aliases": [
"tim-reddy:starr-seq-construct-lib-P016"
],
"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": "2025-04-09T16:39:50.733194+00:00",
"sample_summary": "Homo sapiens K562 cell line, transfected with a reporter library",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8103VLQU/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8103VLQU",
"aliases": [
"tim-reddy:starr-seq-k562-P016"
],
"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": "2025-02-06T14:26:55.813707+00:00",
"summary": "SUPERSTARR: alignments, index, reporter genomic variant effects, reporter variants",
"uuid": "d41f78e7-344a-4111-b3ec-bca5a422008d",
"workflows": [
{
"@id": "/workflows/IGVFWF6957ZNII/",
"accession": "IGVFWF6957ZNII",
"name": "SUPERSTARR Pipeline",
"status": "in progress",
"uniform_pipeline": false
}
]
}