{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS5620SSUW/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS5620SSUW",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF1-BinC-PCR1-Rep1_S3",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF1-BinC-PCR2-Rep1_S9",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF1-BinC-PCR3-Rep1_S57",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF1-BinC-PCR4-Rep1_S63"
],
"audit": {
"NOT_COMPLIANT": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS5620SSUW](/auxiliary-sets/IGVFDS5620SSUW/) has sequence file(s) [IGVFFI6659FRJR](/sequence-files/IGVFFI6659FRJR/), [IGVFFI6031KNOJ](/sequence-files/IGVFFI6031KNOJ/), [IGVFFI1892YSAR](/sequence-files/IGVFFI1892YSAR/), [IGVFFI3345DMYE](/sequence-files/IGVFFI3345DMYE/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS5620SSUW/"
}
]
},
"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": "2024-05-14T20:30:54.584462+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/IGVFFI6659FRJR/",
"accession": "IGVFFI6659FRJR",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF1-BinC-PCR1-Rep1_S3"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:44:41.446225+00:00",
"file_format": "fastq",
"file_size": 26272402,
"href": "/sequence-files/IGVFFI6659FRJR/@@download/IGVFFI6659FRJR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/fad7babe-708a-44be-a758-4cd1058a0cf1/IGVFFI6659FRJR.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin0hrs-FF1-BinC-PCR1-Rep1_S3_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0077VRGD/",
"accession": "IGVFFI0077VRGD",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF1-BinC-PCR1-Rep1_S3"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:37:21.923731+00:00",
"file_format": "yaml",
"file_size": 910,
"href": "/configuration-files/IGVFFI0077VRGD/@@download/IGVFFI0077VRGD.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/a6d52adb-4738-4ffb-8718-96e584303872/IGVFFI0077VRGD.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF1-BinC-PCR1-Rep1_S3.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2971NFJT/",
"accession": "IGVFFI2971NFJT",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF1-BinC-PCR2-Rep1_S9"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:37:36.322023+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI2971NFJT/@@download/IGVFFI2971NFJT.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/9233e2ae-4e15-4f2a-9156-0b4a1d2f5ed1/IGVFFI2971NFJT.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF1-BinC-PCR2-Rep1_S9.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6031KNOJ/",
"accession": "IGVFFI6031KNOJ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF1-BinC-PCR2-Rep1_S9"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:44:59.751696+00:00",
"file_format": "fastq",
"file_size": 30371696,
"href": "/sequence-files/IGVFFI6031KNOJ/@@download/IGVFFI6031KNOJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/5ba3dacd-c4e3-44d3-a94e-c4d1fb5c0fef/IGVFFI6031KNOJ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin0hrs-FF1-BinC-PCR2-Rep1_S9_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1892YSAR/",
"accession": "IGVFFI1892YSAR",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF1-BinC-PCR3-Rep1_S57"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:45:17.855964+00:00",
"file_format": "fastq",
"file_size": 24489960,
"href": "/sequence-files/IGVFFI1892YSAR/@@download/IGVFFI1892YSAR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/388be74e-c3b6-4a0e-92f0-31ea3c91e40b/IGVFFI1892YSAR.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin0hrs-FF1-BinC-PCR3-Rep1_S57_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3345DMYE/",
"accession": "IGVFFI3345DMYE",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF1-BinC-PCR4-Rep1_S63"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:45:35.704601+00:00",
"file_format": "fastq",
"file_size": 27780314,
"href": "/sequence-files/IGVFFI3345DMYE/@@download/IGVFFI3345DMYE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/3e496877-2eec-41c5-bdc5-75ae340ba17f/IGVFFI3345DMYE.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin0hrs-FF1-BinC-PCR4-Rep1_S63_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7355CETE/",
"accession": "IGVFFI7355CETE",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF1-BinC-PCR3-Rep1_S57"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:37:51.839359+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI7355CETE/@@download/IGVFFI7355CETE.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/c547a31a-309a-44e4-812c-39d36d7b5f10/IGVFFI7355CETE.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF1-BinC-PCR3-Rep1_S57.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3038ATER/",
"accession": "IGVFFI3038ATER",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF1-BinC-PCR4-Rep1_S63"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:38:07.326392+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI3038ATER/@@download/IGVFFI3038ATER.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/04d7adfc-e2f9-439a-b17b-0b0b324e6d12/IGVFFI3038ATER.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF1-BinC-PCR4-Rep1_S63.yaml",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS2031CTSP/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS9212JUFJ/",
"accession": "IGVFDS9212JUFJ",
"aliases": [
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinC-PCR1-Rep1_S3",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinC-PCR2-Rep1_S9",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinC-PCR3-Rep1_S57",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinC-PCR4-Rep1_S63"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:23:55.797493+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7889BDAF/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7889BDAF",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinC-PCR1-Rep1_S3",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinC-PCR2-Rep1_S9",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinC-PCR3-Rep1_S57",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinC-PCR4-Rep1_S63"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS5413RKIA/"
],
"modifications": [
{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
"modality": "interference"
},
{
"@id": "/degron-modifications/2e8d10cc-fc98-44d5-a7d9-e2892e16c98a/",
"modality": "degradation"
}
],
"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 SSFA2) modified with CRISPRi Sp-dCas9-KOX1-KRAB, inactive AID system targeting RAD21, transfected with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "11",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-01T01:44:41.446225+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "f918bd18-c0f4-4498-a88f-5eff15b08367"
}