{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS1748WPZO/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS1748WPZO",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR1_Rep1_S139",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR1_Rep2_S194",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR2_Rep1_S145",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR2_Rep2_S200",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR3_Rep1_S151",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR3_Rep2_S206",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR4_Rep1_S157",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR4_Rep2_S212"
],
"audit": {
"NOT_COMPLIANT": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS1748WPZO](/auxiliary-sets/IGVFDS1748WPZO/) has sequence file(s) [IGVFFI7918JLEC](/sequence-files/IGVFFI7918JLEC/), [IGVFFI4124LZQS](/sequence-files/IGVFFI4124LZQS/), [IGVFFI1556PTKF](/sequence-files/IGVFFI1556PTKF/), [IGVFFI6201YBUU](/sequence-files/IGVFFI6201YBUU/), [IGVFFI0138SEGI](/sequence-files/IGVFFI0138SEGI/), [IGVFFI7692ITME](/sequence-files/IGVFFI7692ITME/), [IGVFFI7499BCPY](/sequence-files/IGVFFI7499BCPY/), [IGVFFI4194ZWJO](/sequence-files/IGVFFI4194ZWJO/) 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/IGVFDS1748WPZO/"
}
]
},
"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"
},
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"creation_timestamp": "2024-05-21T17:40:00.726262+00:00",
"donors": [
{
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"aliases": [
"igvf:donor_of_HCT116"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "gRNA sequencing",
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{
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],
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"upload_status": "validated"
},
{
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],
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"upload_status": "validated"
},
{
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],
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1556PTKF/",
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],
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2553TBGP/",
"accession": "IGVFFI2553TBGP",
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"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR1_Rep2_S194"
],
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"s3_uri": "s3://igvf-files/2024/06/11/a5708691-359f-491a-bb9f-d67f31ebb66f/IGVFFI2553TBGP.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF2-BinE-PCR1_Rep2_S194.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7752ZHQN/",
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],
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6201YBUU/",
"accession": "IGVFFI6201YBUU",
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],
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"upload_status": "validated"
},
{
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],
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"upload_status": "validated"
},
{
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],
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"upload_status": "validated"
},
{
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],
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},
{
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},
{
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},
{
"@id": "/configuration-files/IGVFFI2298KKLO/",
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},
{
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7084UIRR/",
"accession": "IGVFFI7084UIRR",
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],
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9686UZVW/",
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],
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"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4544YEQM/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
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"accession": "IGVFDS8267KGLQ",
"aliases": [
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"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR1_Rep2_S194",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR2_Rep1_S145",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR2_Rep2_S200",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR3_Rep1_S151",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR3_Rep2_S206",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR4_Rep1_S157",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR4_Rep2_S212"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:22:02.766281+00:00",
"samples": [
{
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"@type": [
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"Biosample",
"Sample",
"Item"
],
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"aliases": [
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"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR1_Rep2_S194",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR2_Rep1_S145",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR2_Rep2_S200",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR3_Rep1_S151",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR3_Rep2_S206",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR4_Rep1_S157",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR4_Rep2_S212"
],
"classifications": [
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],
"construct_library_sets": [
"/construct-library-sets/IGVFDS7857SYCK/"
],
"modifications": [
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"/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/"
],
"sample_terms": [
{
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"@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 MYC) 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": [
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]
}
],
"schema_version": "11",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-01T02:06:28.028692+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "5735424e-47f5-4b5f-a9f1-b2894489f0a8"
}