{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS1008MWKE/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS1008MWKE",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF2-BinB-PCR1_S62",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF2-BinB-PCR2_S68",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF2-BinB-PCR3_S158",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF2-BinB-PCR4_S164"
],
"audit": {
"NOT_COMPLIANT": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS1008MWKE](/auxiliary-sets/IGVFDS1008MWKE/) has sequence file(s) [IGVFFI2462KGZI](/sequence-files/IGVFFI2462KGZI/), [IGVFFI1326FOXQ](/sequence-files/IGVFFI1326FOXQ/), [IGVFFI7411OJZE](/sequence-files/IGVFFI7411OJZE/), [IGVFFI2595DTOA](/sequence-files/IGVFFI2595DTOA/) 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/IGVFDS1008MWKE/"
}
]
},
"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": "2024-05-16T17:59:35.951142+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/IGVFFI2462KGZI/",
"accession": "IGVFFI2462KGZI",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF2-BinB-PCR1_S62"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T15:22:28.935540+00:00",
"file_format": "fastq",
"file_size": 15992476,
"href": "/sequence-files/IGVFFI2462KGZI/@@download/IGVFFI2462KGZI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/7e7d6514-bcae-4ab7-9805-5169c11ace97/IGVFFI2462KGZI.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF2-BinB-PCR1_S62_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6604LVOF/",
"accession": "IGVFFI6604LVOF",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF2-BinB-PCR1_S62"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:10:20.701175+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI6604LVOF/@@download/IGVFFI6604LVOF.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/7931a811-2f0b-46de-b283-35ee16597c35/IGVFFI6604LVOF.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF2-BinB-PCR1_S62.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1326FOXQ/",
"accession": "IGVFFI1326FOXQ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF2-BinB-PCR4_S164"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T15:26:30.302441+00:00",
"file_format": "fastq",
"file_size": 19755910,
"href": "/sequence-files/IGVFFI1326FOXQ/@@download/IGVFFI1326FOXQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/d9b12ef3-1c9f-43d9-a553-93e7a2fbc126/IGVFFI1326FOXQ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF2-BinB-PCR4_S164_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7411OJZE/",
"accession": "IGVFFI7411OJZE",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF2-BinB-PCR2_S68"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T15:22:45.889065+00:00",
"file_format": "fastq",
"file_size": 12336642,
"href": "/sequence-files/IGVFFI7411OJZE/@@download/IGVFFI7411OJZE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/11774e2c-d219-4a65-895c-260c5d3b11b2/IGVFFI7411OJZE.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF2-BinB-PCR2_S68_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2595DTOA/",
"accession": "IGVFFI2595DTOA",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF2-BinB-PCR3_S158"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T15:26:09.325596+00:00",
"file_format": "fastq",
"file_size": 25592663,
"href": "/sequence-files/IGVFFI2595DTOA/@@download/IGVFFI2595DTOA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/428472d2-4963-4c4a-a1cd-d087b210806d/IGVFFI2595DTOA.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF2-BinB-PCR3_S158_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8100TPVI/",
"accession": "IGVFFI8100TPVI",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF2-BinB-PCR3_S158"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:10:50.516145+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI8100TPVI/@@download/IGVFFI8100TPVI.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/85f3be8a-1036-4171-8a4b-a96d4f68ecf1/IGVFFI8100TPVI.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF2-BinB-PCR3_S158.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6970XEOM/",
"accession": "IGVFFI6970XEOM",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF2-BinB-PCR2_S68"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:10:35.677337+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI6970XEOM/@@download/IGVFFI6970XEOM.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/45d426a7-a568-456e-9695-f9d548085c6c/IGVFFI6970XEOM.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF2-BinB-PCR2_S68.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4650RNWL/",
"accession": "IGVFFI4650RNWL",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF2-BinB-PCR4_S164"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:11:07.437880+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI4650RNWL/@@download/IGVFFI4650RNWL.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/711d8dee-0376-4f32-9ffc-08deed6d2114/IGVFFI4650RNWL.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF2-BinB-PCR4_S164.yaml",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS6482AXWW/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS1817YVNX/",
"accession": "IGVFDS1817YVNX",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF2-BinB-PCR1_S62",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF2-BinB-PCR2_S68",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF2-BinB-PCR3_S158",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF2-BinB-PCR4_S164"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:17:11.951260+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9298VRIP/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9298VRIP",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF2-BinB-PCR1_S62",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF2-BinB-PCR2_S68",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF2-BinB-PCR3_S158",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF2-BinB-PCR4_S164"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS7846UISG/"
],
"modifications": [
{
"@id": "/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/",
"modality": "degradation"
},
{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
"modality": "interference"
}
],
"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 B for 10-20% 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/",
"treatment_term_name": "5-Phenyl-1H-indole-3-acetic acid"
}
]
}
],
"schema_version": "11",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-03T15:22:28.935540+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "ef96cc3b-2401-4dd5-b19e-e4879d72988d"
}