{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS1575SRMY/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS1575SRMY",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF4-BinE-PCR1_S41",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF4-BinE-PCR2_S47",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF4-BinE-PCR3_S137",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF4-BinE-PCR4_S143"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS1575SRMY](/auxiliary-sets/IGVFDS1575SRMY/) has sequence file(s) [IGVFFI0294ZOLF](/sequence-files/IGVFFI0294ZOLF/), [IGVFFI6643VIJQ](/sequence-files/IGVFFI6643VIJQ/), [IGVFFI7817UFSJ](/sequence-files/IGVFFI7817UFSJ/), [IGVFFI9654OFFE](/sequence-files/IGVFFI9654OFFE/) 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/IGVFDS1575SRMY/"
}
]
},
"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": "2024-05-16T17:42:32.230283+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/IGVFFI0294ZOLF/",
"accession": "IGVFFI0294ZOLF",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF4-BinE-PCR1_S41"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:18:53.073476+00:00",
"file_format": "fastq",
"file_size": 9518768,
"href": "/sequence-files/IGVFFI0294ZOLF/@@download/IGVFFI0294ZOLF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/e1a76f3e-fa75-4cff-b08c-ffc077e5d5ee/IGVFFI0294ZOLF.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-FF4-BinE-PCR1_S41_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9076ESKZ/",
"accession": "IGVFFI9076ESKZ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF4-BinE-PCR1_S41"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:08:30.992087+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI9076ESKZ/@@download/IGVFFI9076ESKZ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/91635fe9-7304-42c0-9e38-3d8f31d45bba/IGVFFI9076ESKZ.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF4-BinE-PCR1_S41.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6643VIJQ/",
"accession": "IGVFFI6643VIJQ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF4-BinE-PCR3_S137"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:19:30.478027+00:00",
"file_format": "fastq",
"file_size": 15894366,
"href": "/sequence-files/IGVFFI6643VIJQ/@@download/IGVFFI6643VIJQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/7247bc29-b627-48bb-8c76-c9ad99520c76/IGVFFI6643VIJQ.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-FF4-BinE-PCR3_S137_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7817UFSJ/",
"accession": "IGVFFI7817UFSJ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF4-BinE-PCR4_S143"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:19:48.827747+00:00",
"file_format": "fastq",
"file_size": 15082646,
"href": "/sequence-files/IGVFFI7817UFSJ/@@download/IGVFFI7817UFSJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/62a0fcdf-842e-4923-aea2-798391c45343/IGVFFI7817UFSJ.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-FF4-BinE-PCR4_S143_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9654OFFE/",
"accession": "IGVFFI9654OFFE",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF4-BinE-PCR2_S47"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:19:12.571485+00:00",
"file_format": "fastq",
"file_size": 6769660,
"href": "/sequence-files/IGVFFI9654OFFE/@@download/IGVFFI9654OFFE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/95771f19-b6e4-459f-b907-b4a4991b5fad/IGVFFI9654OFFE.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-FF4-BinE-PCR2_S47_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1298TKBV/",
"accession": "IGVFFI1298TKBV",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF4-BinE-PCR4_S143"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:09:13.633917+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI1298TKBV/@@download/IGVFFI1298TKBV.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/ea89ce78-786c-4299-8004-3920d465af4f/IGVFFI1298TKBV.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF4-BinE-PCR4_S143.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1543ISBB/",
"accession": "IGVFFI1543ISBB",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF4-BinE-PCR3_S137"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:08:59.111647+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI1543ISBB/@@download/IGVFFI1543ISBB.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/0d68419b-ada5-452f-91d9-f1c96254f930/IGVFFI1543ISBB.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF4-BinE-PCR3_S137.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7790ILMG/",
"accession": "IGVFFI7790ILMG",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF4-BinE-PCR2_S47"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:08:44.789169+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI7790ILMG/@@download/IGVFFI7790ILMG.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/c334cbe1-d01c-471c-baa7-7affccc8448c/IGVFFI7790ILMG.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF4-BinE-PCR2_S47.yaml",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS6482AXWW/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS3215BSOP/",
"accession": "IGVFDS3215BSOP",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF4-BinE-PCR1_S41",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF4-BinE-PCR2_S47",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF4-BinE-PCR3_S137",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF4-BinE-PCR4_S143"
],
"preferred_assay_title": "CRISPR FlowFISH screen",
"status": "released"
}
],
"release_timestamp": "2024-07-10T20:16:07.637188+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3377SBLH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3377SBLH",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinE-PCR1_S41",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinE-PCR2_S47",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinE-PCR3_S137",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinE-PCR4_S143"
],
"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 E for 80-90% 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": "2024-06-01T02:18:53.073476+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "d36670f3-17ec-4f7a-a7c7-f361459b5245"
}