{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS1862OQFF/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS1862OQFF",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF3-BinC-PCR1_S27",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF3-BinC-PCR2_S33",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF3-BinC-PCR3_S123",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF3-BinC-PCR4_S129"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS1862OQFF](/auxiliary-sets/IGVFDS1862OQFF/) has sequence file(s) [IGVFFI4922WJWK](/sequence-files/IGVFFI4922WJWK/), [IGVFFI6170DQVL](/sequence-files/IGVFFI6170DQVL/), [IGVFFI2920YFXU](/sequence-files/IGVFFI2920YFXU/), [IGVFFI2665CFFL](/sequence-files/IGVFFI2665CFFL/) 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/IGVFDS1862OQFF/"
}
]
},
"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": "2024-05-16T17:41:58.552592+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/IGVFFI4922WJWK/",
"accession": "IGVFFI4922WJWK",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF3-BinC-PCR1_S27"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:17:31.180855+00:00",
"file_format": "fastq",
"file_size": 8319942,
"href": "/sequence-files/IGVFFI4922WJWK/@@download/IGVFFI4922WJWK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/ac954d00-d0df-4313-8ebc-28f8017035b9/IGVFFI4922WJWK.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF3-BinC-PCR1_S27_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9983TVLX/",
"accession": "IGVFFI9983TVLX",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF3-BinC-PCR1_S27"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:07:33.527925+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI9983TVLX/@@download/IGVFFI9983TVLX.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/6622a421-c4a1-4bdd-a32f-04528f7fd83f/IGVFFI9983TVLX.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF3-BinC-PCR1_S27.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6170DQVL/",
"accession": "IGVFFI6170DQVL",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF3-BinC-PCR2_S33"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:17:48.748083+00:00",
"file_format": "fastq",
"file_size": 8588995,
"href": "/sequence-files/IGVFFI6170DQVL/@@download/IGVFFI6170DQVL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/085c1a0c-bc65-48ca-a268-256d4f1c5dc5/IGVFFI6170DQVL.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF3-BinC-PCR2_S33_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2920YFXU/",
"accession": "IGVFFI2920YFXU",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF3-BinC-PCR3_S123"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:18:06.711793+00:00",
"file_format": "fastq",
"file_size": 24496028,
"href": "/sequence-files/IGVFFI2920YFXU/@@download/IGVFFI2920YFXU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/92fa413b-d6dd-445d-89ee-1b37fe6658fb/IGVFFI2920YFXU.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF3-BinC-PCR3_S123_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2665CFFL/",
"accession": "IGVFFI2665CFFL",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF3-BinC-PCR4_S129"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:18:24.581972+00:00",
"file_format": "fastq",
"file_size": 24490302,
"href": "/sequence-files/IGVFFI2665CFFL/@@download/IGVFFI2665CFFL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/4cfced4d-3253-4a3e-96df-3bcb5ac46fb3/IGVFFI2665CFFL.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF3-BinC-PCR4_S129_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8902XMJH/",
"accession": "IGVFFI8902XMJH",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF3-BinC-PCR3_S123"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:08:00.159650+00:00",
"file_format": "yaml",
"file_size": 904,
"href": "/configuration-files/IGVFFI8902XMJH/@@download/IGVFFI8902XMJH.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/40ab03e1-87c1-49c5-bce2-f97f4551c75e/IGVFFI8902XMJH.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF3-BinC-PCR3_S123.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4440NMXK/",
"accession": "IGVFFI4440NMXK",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF3-BinC-PCR4_S129"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:08:13.393273+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI4440NMXK/@@download/IGVFFI4440NMXK.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/597f578e-66ec-4f4b-a3f4-0f150b5b4774/IGVFFI4440NMXK.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF3-BinC-PCR4_S129.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1027JRLX/",
"accession": "IGVFFI1027JRLX",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF3-BinC-PCR2_S33"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:07:46.950814+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI1027JRLX/@@download/IGVFFI1027JRLX.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/24015ed1-016d-4026-a6b7-43504b203c8d/IGVFFI1027JRLX.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF3-BinC-PCR2_S33.yaml",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS6482AXWW/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS3143OSQG/",
"accession": "IGVFDS3143OSQG",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF3-BinC-PCR1_S27",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF3-BinC-PCR2_S33",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF3-BinC-PCR3_S123",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF3-BinC-PCR4_S129"
],
"preferred_assay_title": "CRISPR FlowFISH screen",
"status": "released"
}
],
"release_timestamp": "2024-07-10T20:15:10.400669+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0811AZWF/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0811AZWF",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF3-BinC-PCR1_S27",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF3-BinC-PCR2_S33",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF3-BinC-PCR3_S123",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF3-BinC-PCR4_S129"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS7846UISG/"
],
"modifications": [
{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
"modality": "interference",
"status": "released"
},
{
"@id": "/degron-modifications/2e8d10cc-fc98-44d5-a7d9-e2892e16c98a/",
"modality": "degradation",
"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 (sorting details: FACS bin C for 35-45% expression of KITLG) modified with CRISPRi Sp-dCas9-KOX1-KRAB, inactive AID system targeting RAD21, transfected with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "12",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-01T02:17:31.180855+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "b907157f-c806-4386-88d0-ff4640e9f0e4"
}