{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS5533XJRU/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS5533XJRU",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_TAPseq-Auxin6hrs-Rep1"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS5533XJRU](/auxiliary-sets/IGVFDS5533XJRU/) has sequence file(s) [IGVFFI7012CCWR](/sequence-files/IGVFFI7012CCWR/), [IGVFFI7666EOCK](/sequence-files/IGVFFI7666EOCK/), [IGVFFI4762FVTH](/sequence-files/IGVFFI4762FVTH/), [IGVFFI0675WIPQ](/sequence-files/IGVFFI0675WIPQ/), [IGVFFI4105QVFH](/sequence-files/IGVFFI4105QVFH/), [IGVFFI1421DDQV](/sequence-files/IGVFFI1421DDQV/), [IGVFFI8910PMMH](/sequence-files/IGVFFI8910PMMH/), [IGVFFI5484ZXJH](/sequence-files/IGVFFI5484ZXJH/), [IGVFFI7147GVXA](/sequence-files/IGVFFI7147GVXA/), [IGVFFI2954POWQ](/sequence-files/IGVFFI2954POWQ/), [IGVFFI2914SEZO](/sequence-files/IGVFFI2914SEZO/), [IGVFFI1192NXTI](/sequence-files/IGVFFI1192NXTI/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS5533XJRU/"
}
]
},
"award": {
"@id": "/awards/HG011972/",
"component": "functional characterization",
"contact_pi": {
"@id": "/users/6c75dbfa-635e-4a7a-8ec8-9e51e9c380a4/",
"title": "Jesse Engreitz"
},
"title": "Stanford Center for Connecting DNA Variants to Function and Phenotype"
},
"control_for": [],
"creation_timestamp": "2024-05-23T22:33:53.437470+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO0384OZRW/",
"accession": "IGVFDO0384OZRW",
"aliases": [
"igvf:donor_of_HCT116"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "gRNA sequencing",
"files": [
{
"@id": "/sequence-files/IGVFFI7012CCWR/",
"accession": "IGVFFI7012CCWR",
"aliases": [
"jesse-engreitz:auxiliary_files_CRUDO_TAPseq-Auxin6hrs-Rep1_S1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T19:15:28.173145+00:00",
"file_format": "fastq",
"file_size": 412697017,
"href": "/sequence-files/IGVFFI7012CCWR/@@download/IGVFFI7012CCWR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/2ea848bc-aed6-4d75-8018-426e4c0ffee0/IGVFFI7012CCWR.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008566/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/221125_Cohesin_TAPseq_v1/221125_Cohesin_TAPseq_v1/outs/fastq_path/L363_S4_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7666EOCK/",
"accession": "IGVFFI7666EOCK",
"aliases": [
"jesse-engreitz:auxiliary_files_CRUDO_TAPseq-Auxin6hrs-Rep1_S1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T19:15:24.292667+00:00",
"file_format": "fastq",
"file_size": 224660683,
"href": "/sequence-files/IGVFFI7666EOCK/@@download/IGVFFI7666EOCK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/59ff1f61-8db2-4aec-9261-ab66750723c0/IGVFFI7666EOCK.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008566/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/221125_Cohesin_TAPseq_v1/221125_Cohesin_TAPseq_v1/outs/fastq_path/L363_S4_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4762FVTH/",
"accession": "IGVFFI4762FVTH",
"aliases": [
"jesse-engreitz:auxiliary_files_CRUDO_TAPseq-Auxin6hrs-Rep1_S4_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T19:16:08.330776+00:00",
"file_format": "fastq",
"file_size": 413548594,
"href": "/sequence-files/IGVFFI4762FVTH/@@download/IGVFFI4762FVTH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/edf4eb2d-9935-43b0-857f-58265d2f18a4/IGVFFI4762FVTH.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008566/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/221125_Cohesin_TAPseq_v1/221125_Cohesin_TAPseq_v1/outs/fastq_path/L363_S4_L004_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0675WIPQ/",
"accession": "IGVFFI0675WIPQ",
"aliases": [
"jesse-engreitz:auxiliary_files_CRUDO_TAPseq-Auxin6hrs-Rep1_S2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T19:15:46.055456+00:00",
"file_format": "fastq",
"file_size": 71911219,
"href": "/sequence-files/IGVFFI0675WIPQ/@@download/IGVFFI0675WIPQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/23c6418f-739e-4b73-b93f-76fc275f52e2/IGVFFI0675WIPQ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008566/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/221125_Cohesin_TAPseq_v1/221125_Cohesin_TAPseq_v1/outs/fastq_path/L363_S4_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4105QVFH/",
"accession": "IGVFFI4105QVFH",
"aliases": [
"jesse-engreitz:auxiliary_files_CRUDO_TAPseq-Auxin6hrs-Rep1_S3_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T19:15:49.335987+00:00",
"file_format": "fastq",
"file_size": 231801394,
"href": "/sequence-files/IGVFFI4105QVFH/@@download/IGVFFI4105QVFH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/1a606357-5938-4780-9821-77374a999f49/IGVFFI4105QVFH.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008566/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/221125_Cohesin_TAPseq_v1/221125_Cohesin_TAPseq_v1/outs/fastq_path/L363_S4_L003_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1421DDQV/",
"accession": "IGVFFI1421DDQV",
"aliases": [
"jesse-engreitz:auxiliary_files_CRUDO_TAPseq-Auxin6hrs-Rep1_S3_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T19:15:55.904273+00:00",
"file_format": "fastq",
"file_size": 414535195,
"href": "/sequence-files/IGVFFI1421DDQV/@@download/IGVFFI1421DDQV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/5de543c2-3848-45cb-9f9b-efdf428be4df/IGVFFI1421DDQV.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008566/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/221125_Cohesin_TAPseq_v1/221125_Cohesin_TAPseq_v1/outs/fastq_path/L363_S4_L003_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8910PMMH/",
"accession": "IGVFFI8910PMMH",
"aliases": [
"jesse-engreitz:auxiliary_files_CRUDO_TAPseq-Auxin6hrs-Rep1_S3_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T19:16:00.759249+00:00",
"file_format": "fastq",
"file_size": 74954889,
"href": "/sequence-files/IGVFFI8910PMMH/@@download/IGVFFI8910PMMH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/ea54211a-ec5b-49c8-b98e-d984617cd942/IGVFFI8910PMMH.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008566/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/221125_Cohesin_TAPseq_v1/221125_Cohesin_TAPseq_v1/outs/fastq_path/L363_S4_L003_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5484ZXJH/",
"accession": "IGVFFI5484ZXJH",
"aliases": [
"jesse-engreitz:auxiliary_files_CRUDO_TAPseq-Auxin6hrs-Rep1_S4_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T19:16:04.768428+00:00",
"file_format": "fastq",
"file_size": 229317133,
"href": "/sequence-files/IGVFFI5484ZXJH/@@download/IGVFFI5484ZXJH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/cc2c00e0-c308-43b8-9fa3-c37bdbf1251e/IGVFFI5484ZXJH.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008566/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/221125_Cohesin_TAPseq_v1/221125_Cohesin_TAPseq_v1/outs/fastq_path/L363_S4_L004_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7147GVXA/",
"accession": "IGVFFI7147GVXA",
"aliases": [
"jesse-engreitz:auxiliary_files_CRUDO_TAPseq-Auxin6hrs-Rep1_S4_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T19:16:14.274854+00:00",
"file_format": "fastq",
"file_size": 74334835,
"href": "/sequence-files/IGVFFI7147GVXA/@@download/IGVFFI7147GVXA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/cb77ce9e-bae5-4d63-a334-59596e4a62c1/IGVFFI7147GVXA.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008566/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/221125_Cohesin_TAPseq_v1/221125_Cohesin_TAPseq_v1/outs/fastq_path/L363_S4_L004_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2954POWQ/",
"accession": "IGVFFI2954POWQ",
"aliases": [
"jesse-engreitz:auxiliary_files_CRUDO_TAPseq-Auxin6hrs-Rep1_S1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T19:15:33.293460+00:00",
"file_format": "fastq",
"file_size": 73547074,
"href": "/sequence-files/IGVFFI2954POWQ/@@download/IGVFFI2954POWQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/94388e6e-49d7-46ff-8458-31c2a88756da/IGVFFI2954POWQ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008566/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/221125_Cohesin_TAPseq_v1/221125_Cohesin_TAPseq_v1/outs/fastq_path/L363_S4_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2914SEZO/",
"accession": "IGVFFI2914SEZO",
"aliases": [
"jesse-engreitz:auxiliary_files_CRUDO_TAPseq-Auxin6hrs-Rep1_S2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T19:15:37.462955+00:00",
"file_format": "fastq",
"file_size": 219660339,
"href": "/sequence-files/IGVFFI2914SEZO/@@download/IGVFFI2914SEZO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/c6e8d55d-666a-432c-851d-6c39235f3b66/IGVFFI2914SEZO.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008566/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/221125_Cohesin_TAPseq_v1/221125_Cohesin_TAPseq_v1/outs/fastq_path/L363_S4_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1192NXTI/",
"accession": "IGVFFI1192NXTI",
"aliases": [
"jesse-engreitz:auxiliary_files_CRUDO_TAPseq-Auxin6hrs-Rep1_S2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T19:15:41.323173+00:00",
"file_format": "fastq",
"file_size": 404698398,
"href": "/sequence-files/IGVFFI1192NXTI/@@download/IGVFFI1192NXTI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/3bff841f-977f-45b3-ba85-32e103c73f5e/IGVFFI1192NXTI.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008566/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/221125_Cohesin_TAPseq_v1/221125_Cohesin_TAPseq_v1/outs/fastq_path/L363_S4_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8106AJBG/",
"accession": "IGVFFI8106AJBG",
"aliases": [
"jesse-engreitz:seqspecfile_crispr_CRUDO_TAPseq_Auxin6hrs-Rep1-S2"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-20T17:16:25.362902+00:00",
"file_format": "yaml",
"file_size": 1173,
"href": "/configuration-files/IGVFFI8106AJBG/@@download/IGVFFI8106AJBG.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/20/f612f15c-5ee3-41b1-8768-5ac7a0ab2216/IGVFFI8106AJBG.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/tapseq_seqspec.out.Auxin6hrs-Rep1-S2.crispr.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2187YPQG/",
"accession": "IGVFFI2187YPQG",
"aliases": [
"jesse-engreitz:seqspecfile_crispr_CRUDO_TAPseq_Auxin6hrs-Rep1-S4"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-20T17:16:34.733275+00:00",
"file_format": "yaml",
"file_size": 1170,
"href": "/configuration-files/IGVFFI2187YPQG/@@download/IGVFFI2187YPQG.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/20/41a62a27-5aa8-4cbb-8e20-7ccc3413b924/IGVFFI2187YPQG.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/tapseq_seqspec.out.Auxin6hrs-Rep1-S4.crispr.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4295FGJK/",
"accession": "IGVFFI4295FGJK",
"aliases": [
"jesse-engreitz:seqspecfile_crispr_CRUDO_TAPseq_Auxin6hrs-Rep1-S1"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-20T17:16:20.141730+00:00",
"file_format": "yaml",
"file_size": 1171,
"href": "/configuration-files/IGVFFI4295FGJK/@@download/IGVFFI4295FGJK.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/20/8cfc6d44-cdac-4d19-abff-9bfe3acc9790/IGVFFI4295FGJK.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/tapseq_seqspec.out.Auxin6hrs-Rep1-S1.crispr.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9289WLAJ/",
"accession": "IGVFFI9289WLAJ",
"aliases": [
"jesse-engreitz:seqspecfile_crispr_CRUDO_TAPseq_Auxin6hrs-Rep1-S3"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-20T17:16:30.085775+00:00",
"file_format": "yaml",
"file_size": 1171,
"href": "/configuration-files/IGVFFI9289WLAJ/@@download/IGVFFI9289WLAJ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/20/4d2288f2-5dc4-44d8-89f8-1d6d91627948/IGVFFI9289WLAJ.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/tapseq_seqspec.out.Auxin6hrs-Rep1-S3.crispr.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS5308EMCG/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS6896VSKX/",
"accession": "IGVFDS6896VSKX",
"aliases": [
"jesse-engreitz:measurement_CRUDO_TAPseq-Auxin6hrs-Rep1"
],
"preferred_assay_title": "TAP-seq",
"status": "released"
}
],
"release_timestamp": "2024-07-10T20:26:48.405757+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9983LVUX/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9983LVUX",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_TAPseq-Auxin6hrs-Rep1"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS9869EMNE/"
],
"modifications": [
{
"@id": "/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/",
"modality": "degradation",
"status": "released"
},
{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
"modality": "interference",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002824/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:HCT116"
],
"status": "released",
"summary": "HCT116",
"term_name": "HCT116"
}
],
"status": "released",
"summary": "HCT116 cell line, male, Homo sapiens treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours, modified with AID system targeting RAD21, CRISPRi Sp-dCas9-KOX1-KRAB, transfected with a guide library",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/",
"status": "released",
"treatment_term_name": "5-Phenyl-1H-indole-3-acetic acid"
}
]
}
],
"schema_version": "12",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-03T19:15:24.292667+00:00",
"summary": "gRNA sequencing for mixed CRISPR TAP-seq integrating a guide (sgRNA) library targeting accessible genome regions in 29 genomic loci",
"uuid": "01c3ecb9-d9e9-4a53-935a-0f69eb422bd5"
}