{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS4894APIT/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS4894APIT",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR1_Rep1_S114",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR1_Rep2_S169",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR2_Rep1_S120",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR2_Rep2_S175",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR3_Rep1_S126",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR3_Rep2_S181",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR4_Rep1_S132",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR4_Rep2_S187"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM0373CYTT](/in-vitro-systems/IGVFSM0373CYTT/) has in progress subobject degron modification [95081d1b-08b4-49ed-b324-e53fc43d8456](/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM0373CYTT/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM0373CYTT](/in-vitro-systems/IGVFSM0373CYTT/) has in progress subobject treatment [d35868d1-c45b-49ae-8ff3-a9c0c22551c2](/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM0373CYTT/"
},
{
"category": "mismatched status",
"detail": "Released human donor [IGVFDO0384OZRW](/human-donors/IGVFDO0384OZRW/) has in progress subobject publication [155f24ce-5c2c-4400-8651-da9447eaca25](/publications/155f24ce-5c2c-4400-8651-da9447eaca25/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO0384OZRW/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS4894APIT](/auxiliary-sets/IGVFDS4894APIT/) has sequence file(s) [IGVFFI6767UOHJ](/sequence-files/IGVFFI6767UOHJ/), [IGVFFI1838TDNU](/sequence-files/IGVFFI1838TDNU/), [IGVFFI5888TLGJ](/sequence-files/IGVFFI5888TLGJ/), [IGVFFI4501LVHP](/sequence-files/IGVFFI4501LVHP/), [IGVFFI4677UICJ](/sequence-files/IGVFFI4677UICJ/), [IGVFFI1659OMPY](/sequence-files/IGVFFI1659OMPY/), [IGVFFI1400XMFH](/sequence-files/IGVFFI1400XMFH/), [IGVFFI7202ZYZL](/sequence-files/IGVFFI7202ZYZL/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 40,
"level_name": "WARNING",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS4894APIT/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS4894APIT](/auxiliary-sets/IGVFDS4894APIT/) is a raw data set with files, but is not listed in any `input_file_sets` for any analysis sets. Raw data sets with files are expected to be associated with at least one analysis set.",
"level": 40,
"level_name": "WARNING",
"name": "audit_input_file_set_for",
"path": "/auxiliary-sets/IGVFDS4894APIT/"
}
]
},
"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": "2024-05-21T17:39:10.058079+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO0384OZRW/",
"accession": "IGVFDO0384OZRW",
"aliases": [
"igvf:donor_of_HCT116"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
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{
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"accession": "IGVFFI6767UOHJ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR1_Rep1_S114"
],
"content_type": "reads",
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"file_format": "fastq",
"file_size": 19880026,
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"sequencing_platform": "/platform-terms/EFO_0008565/",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3679ETJZ/",
"accession": "IGVFFI3679ETJZ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR1_Rep1_S114"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:49:28.629750+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI3679ETJZ/@@download/IGVFFI3679ETJZ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/0bf7d9a0-f6db-41c4-9261-b23f4ea8a645/IGVFFI3679ETJZ.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF1-BinD-PCR1_Rep1_S114.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1838TDNU/",
"accession": "IGVFFI1838TDNU",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR4_Rep2_S187"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:06:02.574915+00:00",
"file_format": "fastq",
"file_size": 25094084,
"href": "/sequence-files/IGVFFI1838TDNU/@@download/IGVFFI1838TDNU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/11b3718f-592b-4c68-8d18-d4b9c857c012/IGVFFI1838TDNU.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin6hrs-FF1-BinD-PCR4-Rep2_S187_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5888TLGJ/",
"accession": "IGVFFI5888TLGJ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR3_Rep1_S126"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:05:06.323462+00:00",
"file_format": "fastq",
"file_size": 19626270,
"href": "/sequence-files/IGVFFI5888TLGJ/@@download/IGVFFI5888TLGJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/d2a2e572-8ebc-45a3-897b-a17587234aa1/IGVFFI5888TLGJ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin6hrs-FF1-BinD-PCR3-Rep1_S126_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5910EETS/",
"accession": "IGVFFI5910EETS",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR3_Rep2_S181"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:50:42.397852+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI5910EETS/@@download/IGVFFI5910EETS.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/f8588a9b-e786-4530-aff8-40fc96b7d2c3/IGVFFI5910EETS.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF1-BinD-PCR3_Rep2_S181.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4501LVHP/",
"accession": "IGVFFI4501LVHP",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR1_Rep2_S169"
],
"content_type": "reads",
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"href": "/sequence-files/IGVFFI4501LVHP/@@download/IGVFFI4501LVHP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/252f2881-678d-4453-bf9b-410cfa81e314/IGVFFI4501LVHP.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin6hrs-FF1-BinD-PCR1-Rep2_S169_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4677UICJ/",
"accession": "IGVFFI4677UICJ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR4_Rep1_S132"
],
"content_type": "reads",
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"file_format": "fastq",
"file_size": 26611943,
"href": "/sequence-files/IGVFFI4677UICJ/@@download/IGVFFI4677UICJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/b18230d4-1518-4b15-8403-e2e545e29449/IGVFFI4677UICJ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin6hrs-FF1-BinD-PCR4-Rep1_S132_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1659OMPY/",
"accession": "IGVFFI1659OMPY",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR2_Rep1_S120"
],
"content_type": "reads",
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"file_format": "fastq",
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"href": "/sequence-files/IGVFFI1659OMPY/@@download/IGVFFI1659OMPY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/8954ea77-fd17-4ffc-aa79-c46a70f1a31f/IGVFFI1659OMPY.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1400XMFH/",
"accession": "IGVFFI1400XMFH",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR2_Rep2_S175"
],
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"href": "/sequence-files/IGVFFI1400XMFH/@@download/IGVFFI1400XMFH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/cb61d5e3-3bb2-4fd0-b2a4-2ab9e94a6405/IGVFFI1400XMFH.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7202ZYZL/",
"accession": "IGVFFI7202ZYZL",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR3_Rep2_S181"
],
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"href": "/sequence-files/IGVFFI7202ZYZL/@@download/IGVFFI7202ZYZL.fastq.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4121BJCJ/",
"accession": "IGVFFI4121BJCJ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR1_Rep2_S169"
],
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"file_format": "yaml",
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"href": "/configuration-files/IGVFFI4121BJCJ/@@download/IGVFFI4121BJCJ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/792caddc-e402-43c5-8a4b-c2b6d4ab5cac/IGVFFI4121BJCJ.yaml.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7948HLPP/",
"accession": "IGVFFI7948HLPP",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR4_Rep2_S187"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:51:13.703174+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI7948HLPP/@@download/IGVFFI7948HLPP.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/c6c9cf0e-eea8-40e2-aa63-d0cf384b4081/IGVFFI7948HLPP.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF1-BinD-PCR4_Rep2_S187.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7989FMBQ/",
"accession": "IGVFFI7989FMBQ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR2_Rep1_S120"
],
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1455JJRV/",
"accession": "IGVFFI1455JJRV",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR2_Rep2_S175"
],
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"file_format": "yaml",
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"href": "/configuration-files/IGVFFI1455JJRV/@@download/IGVFFI1455JJRV.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/a4cc0283-f317-4db0-bc66-474590145a78/IGVFFI1455JJRV.yaml.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2455NBTS/",
"accession": "IGVFFI2455NBTS",
"aliases": [
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],
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"file_size": 910,
"href": "/configuration-files/IGVFFI2455NBTS/@@download/IGVFFI2455NBTS.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/1d9b001f-0717-4c4f-8df1-6550b7fad6fe/IGVFFI2455NBTS.yaml.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2204VYTD/",
"accession": "IGVFFI2204VYTD",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR4_Rep1_S132"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:50:57.786455+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI2204VYTD/@@download/IGVFFI2204VYTD.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/5cd253b1-9235-4b1a-8994-44c80972a8d1/IGVFFI2204VYTD.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF1-BinD-PCR4_Rep1_S132.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS2690TTFH/",
"accession": "IGVFDS2690TTFH",
"aliases": [
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR1_Rep1_S114",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR1_Rep2_S169",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR2_Rep1_S120",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR2_Rep2_S175",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR3_Rep1_S126",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR3_Rep2_S181",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR4_Rep1_S132",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR4_Rep2_S187"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:21:10.325514+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0373CYTT/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0373CYTT",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR1_Rep1_S114",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR1_Rep2_S169",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR2_Rep1_S120",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR2_Rep2_S175",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR3_Rep1_S126",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR3_Rep2_S181",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR4_Rep1_S132",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR4_Rep2_S187"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS7857SYCK/"
],
"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 (sorting details: FACS bin D for 55-65% expression of MYC) treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours, modified 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": "2024-06-01T02:03:45.203043+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "5dfd3991-e8d8-4c94-9aaa-be67bdf3ff18"
}