{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS1910ATCF/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS1910ATCF",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF4-BinD-PCR1_S88",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF4-BinD-PCR2_S94",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF4-BinD-PCR3_S184",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF4-BinD-PCR4_S190"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS1910ATCF](/auxiliary-sets/IGVFDS1910ATCF/) has sequence file(s) [IGVFFI8353GKIF](/sequence-files/IGVFFI8353GKIF/), [IGVFFI2965VPYI](/sequence-files/IGVFFI2965VPYI/), [IGVFFI9113CILL](/sequence-files/IGVFFI9113CILL/), [IGVFFI6442YJFK](/sequence-files/IGVFFI6442YJFK/) 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/IGVFDS1910ATCF/"
}
]
},
"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": "2024-05-16T18:01:21.559006+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/IGVFFI8353GKIF/",
"accession": "IGVFFI8353GKIF",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF4-BinD-PCR1_S88"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T15:27:58.996072+00:00",
"file_format": "fastq",
"file_size": 6887653,
"href": "/sequence-files/IGVFFI8353GKIF/@@download/IGVFFI8353GKIF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/d2fdc34c-fad7-466b-a010-60852aae0271/IGVFFI8353GKIF.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-FF4-BinD-PCR1_S88_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2305CMEX/",
"accession": "IGVFFI2305CMEX",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF4-BinD-PCR1_S88"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:12:24.373880+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI2305CMEX/@@download/IGVFFI2305CMEX.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/4c84bf11-932d-4444-9b57-83ba45217718/IGVFFI2305CMEX.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF4-BinD-PCR1_S88.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2965VPYI/",
"accession": "IGVFFI2965VPYI",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF4-BinD-PCR2_S94"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T15:28:15.143246+00:00",
"file_format": "fastq",
"file_size": 6724540,
"href": "/sequence-files/IGVFFI2965VPYI/@@download/IGVFFI2965VPYI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/28494f3e-c085-4e10-8f59-972aff2d6b9b/IGVFFI2965VPYI.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-FF4-BinD-PCR2_S94_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9113CILL/",
"accession": "IGVFFI9113CILL",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF4-BinD-PCR3_S184"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T15:28:31.835592+00:00",
"file_format": "fastq",
"file_size": 12099763,
"href": "/sequence-files/IGVFFI9113CILL/@@download/IGVFFI9113CILL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/fb7c2526-5fa1-4f41-8ad3-e9226566e8b3/IGVFFI9113CILL.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-FF4-BinD-PCR3_S184_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6442YJFK/",
"accession": "IGVFFI6442YJFK",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF4-BinD-PCR4_S190"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T15:28:48.339110+00:00",
"file_format": "fastq",
"file_size": 11917509,
"href": "/sequence-files/IGVFFI6442YJFK/@@download/IGVFFI6442YJFK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/11af4451-c72b-4c5c-b59b-0c47731e1a29/IGVFFI6442YJFK.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-FF4-BinD-PCR4_S190_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0385FMRJ/",
"accession": "IGVFFI0385FMRJ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF4-BinD-PCR4_S190"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:13:08.280274+00:00",
"file_format": "yaml",
"file_size": 904,
"href": "/configuration-files/IGVFFI0385FMRJ/@@download/IGVFFI0385FMRJ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/3330dfb5-d114-4802-b915-9bfbffb49561/IGVFFI0385FMRJ.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF4-BinD-PCR4_S190.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4090ZZUM/",
"accession": "IGVFFI4090ZZUM",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF4-BinD-PCR2_S94"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:12:38.987051+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI4090ZZUM/@@download/IGVFFI4090ZZUM.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/90e9024f-74fc-46e1-8d3d-ef1f2268f1a0/IGVFFI4090ZZUM.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF4-BinD-PCR2_S94.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2638WTSF/",
"accession": "IGVFFI2638WTSF",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF4-BinD-PCR3_S184"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:12:53.595560+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI2638WTSF/@@download/IGVFFI2638WTSF.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/192ff44b-8e14-42e7-9081-2171bd4be1ec/IGVFFI2638WTSF.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF4-BinD-PCR3_S184.yaml",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS6482AXWW/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS9620HBWE/",
"accession": "IGVFDS9620HBWE",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF4-BinD-PCR1_S88",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF4-BinD-PCR2_S94",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF4-BinD-PCR3_S184",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF4-BinD-PCR4_S190"
],
"preferred_assay_title": "CRISPR FlowFISH screen",
"status": "released"
}
],
"release_timestamp": "2024-07-10T20:18:51.124825+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5357VTYO/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5357VTYO",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF4-BinD-PCR1_S88",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF4-BinD-PCR2_S94",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF4-BinD-PCR3_S184",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF4-BinD-PCR4_S190"
],
"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 D for 55-65% 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": "2024-06-03T15:27:58.996072+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "03f67d35-481a-4f0b-bdba-72187fe3be05"
}