{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS5369WGWJ/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS5369WGWJ",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF3-BinF-PCR1_S78",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF3-BinF-PCR2_S84",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF3-BinF-PCR3_S174",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF3-BinF-PCR4_S180"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS5369WGWJ](/auxiliary-sets/IGVFDS5369WGWJ/) has sequence file(s) [IGVFFI4045TUNG](/sequence-files/IGVFFI4045TUNG/), [IGVFFI6628WMUK](/sequence-files/IGVFFI6628WMUK/), [IGVFFI0124JBXT](/sequence-files/IGVFFI0124JBXT/), [IGVFFI3098GZST](/sequence-files/IGVFFI3098GZST/) 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/IGVFDS5369WGWJ/"
}
]
},
"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": "2024-05-16T18:01:01.326329+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/IGVFFI4045TUNG/",
"accession": "IGVFFI4045TUNG",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF3-BinF-PCR1_S78"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T15:26:58.560343+00:00",
"file_format": "fastq",
"file_size": 6161068,
"href": "/sequence-files/IGVFFI4045TUNG/@@download/IGVFFI4045TUNG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/356cb3e0-8c2b-4e1b-bd38-c6e0f3c731db/IGVFFI4045TUNG.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF3-BinF-PCR1_S78_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6854JPHC/",
"accession": "IGVFFI6854JPHC",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF3-BinF-PCR1_S78"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:11:31.305329+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI6854JPHC/@@download/IGVFFI6854JPHC.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/4efa666a-f5de-4e8a-8e18-b6c0a51add5d/IGVFFI6854JPHC.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF3-BinF-PCR1_S78.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6628WMUK/",
"accession": "IGVFFI6628WMUK",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF3-BinF-PCR2_S84"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T15:27:14.302971+00:00",
"file_format": "fastq",
"file_size": 7441200,
"href": "/sequence-files/IGVFFI6628WMUK/@@download/IGVFFI6628WMUK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/fb4209bb-eff5-4287-80c6-e2f9f72a75e0/IGVFFI6628WMUK.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF3-BinF-PCR2_S84_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0124JBXT/",
"accession": "IGVFFI0124JBXT",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF3-BinF-PCR3_S174"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T15:27:31.177759+00:00",
"file_format": "fastq",
"file_size": 11459243,
"href": "/sequence-files/IGVFFI0124JBXT/@@download/IGVFFI0124JBXT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/8761ab09-b3ba-43ae-b8b3-df04f6bb86fe/IGVFFI0124JBXT.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF3-BinF-PCR3_S174_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3098GZST/",
"accession": "IGVFFI3098GZST",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF3-BinF-PCR4_S180"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T15:27:48.233804+00:00",
"file_format": "fastq",
"file_size": 16266225,
"href": "/sequence-files/IGVFFI3098GZST/@@download/IGVFFI3098GZST.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/b5aa5385-b44c-4dc7-99d0-106dc275183d/IGVFFI3098GZST.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF3-BinF-PCR4_S180_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6268PNTT/",
"accession": "IGVFFI6268PNTT",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF3-BinF-PCR3_S174"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:12:00.499211+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI6268PNTT/@@download/IGVFFI6268PNTT.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/7b3c274b-5d13-44fe-ab43-2bc036b56787/IGVFFI6268PNTT.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF3-BinF-PCR3_S174.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2186WCZI/",
"accession": "IGVFFI2186WCZI",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF3-BinF-PCR4_S180"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:12:14.854748+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI2186WCZI/@@download/IGVFFI2186WCZI.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/e8c15e5b-8611-4087-8b98-918017394d21/IGVFFI2186WCZI.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF3-BinF-PCR4_S180.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6824CZPV/",
"accession": "IGVFFI6824CZPV",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF3-BinF-PCR2_S84"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:11:45.893544+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI6824CZPV/@@download/IGVFFI6824CZPV.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/17050ed2-1120-4bda-97d3-ac512b121636/IGVFFI6824CZPV.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF3-BinF-PCR2_S84.yaml",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS6482AXWW/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS6320HMYC/",
"accession": "IGVFDS6320HMYC",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF3-BinF-PCR1_S78",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF3-BinF-PCR2_S84",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF3-BinF-PCR3_S174",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF3-BinF-PCR4_S180"
],
"preferred_assay_title": "CRISPR FlowFISH screen",
"status": "released"
}
],
"release_timestamp": "2024-07-10T20:18:23.074692+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3650ZODU/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3650ZODU",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF3-BinF-PCR1_S78",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF3-BinF-PCR2_S84",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF3-BinF-PCR3_S174",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF3-BinF-PCR4_S180"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS7846UISG/"
],
"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 (sorting details: FACS bin F for 80-100% expression of KITLG) 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": "2024-06-03T15:26:58.560343+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "49323903-2130-4160-93e0-107c2933b3bc"
}