{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS4057PFBU/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS4057PFBU",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_TAPseq-Auxin6hrs-Rep2"
],
"audit": {
"NOT_COMPLIANT": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS4057PFBU](/auxiliary-sets/IGVFDS4057PFBU/) has sequence file(s) [IGVFFI3454BUML](/sequence-files/IGVFFI3454BUML/), [IGVFFI3968OUXL](/sequence-files/IGVFFI3968OUXL/), [IGVFFI4244AIHE](/sequence-files/IGVFFI4244AIHE/), [IGVFFI6509IKAK](/sequence-files/IGVFFI6509IKAK/), [IGVFFI7745NNEZ](/sequence-files/IGVFFI7745NNEZ/), [IGVFFI4261MKPE](/sequence-files/IGVFFI4261MKPE/), [IGVFFI2009UHTY](/sequence-files/IGVFFI2009UHTY/), [IGVFFI7212KPPW](/sequence-files/IGVFFI7212KPPW/), [IGVFFI2734JVZP](/sequence-files/IGVFFI2734JVZP/), [IGVFFI3142LWDR](/sequence-files/IGVFFI3142LWDR/), [IGVFFI6662ZMLA](/sequence-files/IGVFFI6662ZMLA/), [IGVFFI8620YJXA](/sequence-files/IGVFFI8620YJXA/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS4057PFBU/"
}
]
},
"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": "2024-05-23T22:33:55.800312+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/IGVFFI3454BUML/",
"accession": "IGVFFI3454BUML",
"aliases": [
"jesse-engreitz:auxiliary_files_CRUDO_TAPseq-Auxin6hrs-Rep2_S2_R1"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T19:17:10.048409+00:00",
"file_format": "fastq",
"file_size": 72826284,
"href": "/sequence-files/IGVFFI3454BUML/@@download/IGVFFI3454BUML.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/c11e3ed3-ed67-4621-8b10-6ef335a400f5/IGVFFI3454BUML.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008566/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/221224_Cohesin_TAPseq_v2/221219_P044_cohesin_tapseq_v2/outs/fastq_path/L381_S4_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3968OUXL/",
"accession": "IGVFFI3968OUXL",
"aliases": [
"jesse-engreitz:auxiliary_files_CRUDO_TAPseq-Auxin6hrs-Rep2_S1_I1"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T19:17:06.919028+00:00",
"file_format": "fastq",
"file_size": 22349507,
"href": "/sequence-files/IGVFFI3968OUXL/@@download/IGVFFI3968OUXL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/7c86f7b9-89b4-4807-bbdf-3958cf0ee5d0/IGVFFI3968OUXL.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008566/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/221224_Cohesin_TAPseq_v2/221219_P044_cohesin_tapseq_v2/outs/fastq_path/L381_S4_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4244AIHE/",
"accession": "IGVFFI4244AIHE",
"aliases": [
"jesse-engreitz:auxiliary_files_CRUDO_TAPseq-Auxin6hrs-Rep2_S2_I1"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T19:17:16.634689+00:00",
"file_format": "fastq",
"file_size": 22641543,
"href": "/sequence-files/IGVFFI4244AIHE/@@download/IGVFFI4244AIHE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/4011a6d4-3dbe-4889-bd25-dc241429dbab/IGVFFI4244AIHE.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008566/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/221224_Cohesin_TAPseq_v2/221219_P044_cohesin_tapseq_v2/outs/fastq_path/L381_S4_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6509IKAK/",
"accession": "IGVFFI6509IKAK",
"aliases": [
"jesse-engreitz:auxiliary_files_CRUDO_TAPseq-Auxin6hrs-Rep2_S3_R2"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T19:17:22.612277+00:00",
"file_format": "fastq",
"file_size": 133294093,
"href": "/sequence-files/IGVFFI6509IKAK/@@download/IGVFFI6509IKAK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/a9f0e118-49bc-49f1-a1f5-de2d8858a6f9/IGVFFI6509IKAK.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008566/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/221224_Cohesin_TAPseq_v2/221219_P044_cohesin_tapseq_v2/outs/fastq_path/L381_S4_L003_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7745NNEZ/",
"accession": "IGVFFI7745NNEZ",
"aliases": [
"jesse-engreitz:auxiliary_files_CRUDO_TAPseq-Auxin6hrs-Rep2_S4_I1"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T19:17:40.708327+00:00",
"file_format": "fastq",
"file_size": 22524492,
"href": "/sequence-files/IGVFFI7745NNEZ/@@download/IGVFFI7745NNEZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/0ffdbc9f-3511-44fd-85f1-2f4154efcc05/IGVFFI7745NNEZ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008566/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/221224_Cohesin_TAPseq_v2/221219_P044_cohesin_tapseq_v2/outs/fastq_path/L381_S4_L004_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4261MKPE/",
"accession": "IGVFFI4261MKPE",
"aliases": [
"jesse-engreitz:auxiliary_files_CRUDO_TAPseq-Auxin6hrs-Rep2_S1_R2"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T19:17:03.625205+00:00",
"file_format": "fastq",
"file_size": 132182356,
"href": "/sequence-files/IGVFFI4261MKPE/@@download/IGVFFI4261MKPE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/57d10fae-b206-4f93-bbc8-6cc8b1dd7bff/IGVFFI4261MKPE.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008566/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/221224_Cohesin_TAPseq_v2/221219_P044_cohesin_tapseq_v2/outs/fastq_path/L381_S4_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2009UHTY/",
"accession": "IGVFFI2009UHTY",
"aliases": [
"jesse-engreitz:auxiliary_files_CRUDO_TAPseq-Auxin6hrs-Rep2_S2_R2"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T19:17:13.124883+00:00",
"file_format": "fastq",
"file_size": 131865646,
"href": "/sequence-files/IGVFFI2009UHTY/@@download/IGVFFI2009UHTY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/78c0c01f-d10b-418d-8979-c35b07e6129e/IGVFFI2009UHTY.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008566/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/221224_Cohesin_TAPseq_v2/221219_P044_cohesin_tapseq_v2/outs/fastq_path/L381_S4_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7212KPPW/",
"accession": "IGVFFI7212KPPW",
"aliases": [
"jesse-engreitz:auxiliary_files_CRUDO_TAPseq-Auxin6hrs-Rep2_S4_R1"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T19:17:32.937237+00:00",
"file_format": "fastq",
"file_size": 73629654,
"href": "/sequence-files/IGVFFI7212KPPW/@@download/IGVFFI7212KPPW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/3bda2cce-6d21-4053-a465-0ff65c726871/IGVFFI7212KPPW.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008566/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/221224_Cohesin_TAPseq_v2/221219_P044_cohesin_tapseq_v2/outs/fastq_path/L381_S4_L004_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2734JVZP/",
"accession": "IGVFFI2734JVZP",
"aliases": [
"jesse-engreitz:auxiliary_files_CRUDO_TAPseq-Auxin6hrs-Rep2_S1_R1"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T19:17:00.411968+00:00",
"file_format": "fastq",
"file_size": 72462959,
"href": "/sequence-files/IGVFFI2734JVZP/@@download/IGVFFI2734JVZP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/2eaa3703-1de4-46fa-a634-964d96322ef6/IGVFFI2734JVZP.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008566/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/221224_Cohesin_TAPseq_v2/221219_P044_cohesin_tapseq_v2/outs/fastq_path/L381_S4_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3142LWDR/",
"accession": "IGVFFI3142LWDR",
"aliases": [
"jesse-engreitz:auxiliary_files_CRUDO_TAPseq-Auxin6hrs-Rep2_S3_R1"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T19:17:19.600754+00:00",
"file_format": "fastq",
"file_size": 74103059,
"href": "/sequence-files/IGVFFI3142LWDR/@@download/IGVFFI3142LWDR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/5e955e57-7711-448c-a3bf-97fc001175cb/IGVFFI3142LWDR.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008566/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/221224_Cohesin_TAPseq_v2/221219_P044_cohesin_tapseq_v2/outs/fastq_path/L381_S4_L003_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6662ZMLA/",
"accession": "IGVFFI6662ZMLA",
"aliases": [
"jesse-engreitz:auxiliary_files_CRUDO_TAPseq-Auxin6hrs-Rep2_S3_I1"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T19:17:26.245116+00:00",
"file_format": "fastq",
"file_size": 22381194,
"href": "/sequence-files/IGVFFI6662ZMLA/@@download/IGVFFI6662ZMLA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/cc75cf1d-1cc4-4ea9-8022-dcd41c099b72/IGVFFI6662ZMLA.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008566/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/221224_Cohesin_TAPseq_v2/221219_P044_cohesin_tapseq_v2/outs/fastq_path/L381_S4_L003_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8620YJXA/",
"accession": "IGVFFI8620YJXA",
"aliases": [
"jesse-engreitz:auxiliary_files_CRUDO_TAPseq-Auxin6hrs-Rep2_S4_R2"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T19:17:37.408127+00:00",
"file_format": "fastq",
"file_size": 132798687,
"href": "/sequence-files/IGVFFI8620YJXA/@@download/IGVFFI8620YJXA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/9f7fd92d-f075-4cf3-b2df-83cbddd52b5e/IGVFFI8620YJXA.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008566/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/221224_Cohesin_TAPseq_v2/221219_P044_cohesin_tapseq_v2/outs/fastq_path/L381_S4_L004_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5301LVOU/",
"accession": "IGVFFI5301LVOU",
"aliases": [
"jesse-engreitz:seqspecfile_crispr_CRUDO_TAPseq_Auxin6hrs-Rep2-S4"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-20T17:16:54.511503+00:00",
"file_format": "yaml",
"file_size": 1172,
"href": "/configuration-files/IGVFFI5301LVOU/@@download/IGVFFI5301LVOU.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/20/fe962ed8-b778-4568-91b6-c6bb0f0fb82f/IGVFFI5301LVOU.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/tapseq_seqspec.out.Auxin6hrs-Rep2-S4.crispr.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7264CSUJ/",
"accession": "IGVFFI7264CSUJ",
"aliases": [
"jesse-engreitz:seqspecfile_crispr_CRUDO_TAPseq_Auxin6hrs-Rep2-S1"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-20T17:16:39.761519+00:00",
"file_format": "yaml",
"file_size": 1173,
"href": "/configuration-files/IGVFFI7264CSUJ/@@download/IGVFFI7264CSUJ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/20/e844fba0-bfaf-47ff-b2e5-c9c11f2aa668/IGVFFI7264CSUJ.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/tapseq_seqspec.out.Auxin6hrs-Rep2-S1.crispr.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3154ZIRN/",
"accession": "IGVFFI3154ZIRN",
"aliases": [
"jesse-engreitz:seqspecfile_crispr_CRUDO_TAPseq_Auxin6hrs-Rep2-S2"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-20T17:16:44.699537+00:00",
"file_format": "yaml",
"file_size": 1173,
"href": "/configuration-files/IGVFFI3154ZIRN/@@download/IGVFFI3154ZIRN.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/20/54b1fb98-b9c1-4fd2-b5cc-6ab910e3ec2d/IGVFFI3154ZIRN.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/tapseq_seqspec.out.Auxin6hrs-Rep2-S2.crispr.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1570HKMV/",
"accession": "IGVFFI1570HKMV",
"aliases": [
"jesse-engreitz:seqspecfile_crispr_CRUDO_TAPseq_Auxin6hrs-Rep2-S3"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-20T17:16:49.580901+00:00",
"file_format": "yaml",
"file_size": 1173,
"href": "/configuration-files/IGVFFI1570HKMV/@@download/IGVFFI1570HKMV.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/20/2b5c9ef7-bbae-430a-a525-7f31fd797ba6/IGVFFI1570HKMV.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/tapseq_seqspec.out.Auxin6hrs-Rep2-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/IGVFDS8403DDLC/",
"accession": "IGVFDS8403DDLC",
"aliases": [
"jesse-engreitz:measurement_CRUDO_TAPseq-Auxin6hrs-Rep2"
],
"preferred_assay_title": "TAP-seq"
}
],
"release_timestamp": "2024-07-10T20:26:54.948983+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8511JOMW/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8511JOMW",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_TAPseq-Auxin6hrs-Rep2"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS9869EMNE/"
],
"modifications": [
"/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/",
"/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/"
],
"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": [
"/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/"
]
}
],
"schema_version": "11",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-03T19:17:00.411968+00:00",
"summary": "gRNA sequencing for mixed TAP-seq integrating a guide (sgRNA) library targeting accessible genome regions in 29 genomic loci",
"uuid": "6092a5ac-a3ef-4b35-b804-86a28d01b214"
}