{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS6660JNZU/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS6660JNZU",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR1_Rep1_S140",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR1_Rep2_S195",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR2_Rep1_S146",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR2_Rep2_S201",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR3_Rep1_S152",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR3_Rep2_S207",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR4_Rep1_S158",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR4_Rep2_S213"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM3012RMVA](/in-vitro-systems/IGVFSM3012RMVA/) has in progress subobject degron modification [95081d1b-08b4-49ed-b324-e53fc43d8456](/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM3012RMVA/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM3012RMVA](/in-vitro-systems/IGVFSM3012RMVA/) has in progress subobject treatment [d35868d1-c45b-49ae-8ff3-a9c0c22551c2](/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM3012RMVA/"
},
{
"category": "mismatched status",
"detail": "Released human donor [IGVFDO0384OZRW](/human-donors/IGVFDO0384OZRW/) has in progress subobject publication [155f24ce-5c2c-4400-8651-da9447eaca25](/publications/155f24ce-5c2c-4400-8651-da9447eaca25/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO0384OZRW/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS6660JNZU](/auxiliary-sets/IGVFDS6660JNZU/) has sequence file(s) [IGVFFI5709RWIZ](/sequence-files/IGVFFI5709RWIZ/), [IGVFFI2502UDBL](/sequence-files/IGVFFI2502UDBL/), [IGVFFI4385VBWZ](/sequence-files/IGVFFI4385VBWZ/), [IGVFFI9220ZDKH](/sequence-files/IGVFFI9220ZDKH/), [IGVFFI6947RKEO](/sequence-files/IGVFFI6947RKEO/), [IGVFFI9861RLTL](/sequence-files/IGVFFI9861RLTL/), [IGVFFI6772UIRN](/sequence-files/IGVFFI6772UIRN/), [IGVFFI4207NYCN](/sequence-files/IGVFFI4207NYCN/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 40,
"level_name": "WARNING",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS6660JNZU/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS6660JNZU](/auxiliary-sets/IGVFDS6660JNZU/) is a raw data set with files, but is not listed in any `input_file_sets` for any analysis sets. Raw data sets with files are expected to be associated with at least one analysis set.",
"level": 40,
"level_name": "WARNING",
"name": "audit_input_file_set_for",
"path": "/auxiliary-sets/IGVFDS6660JNZU/"
}
]
},
"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": "2024-05-21T17:40:01.657388+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO0384OZRW/",
"accession": "IGVFDO0384OZRW",
"aliases": [
"igvf:donor_of_HCT116"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
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{
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"aliases": [
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],
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"file_format": "fastq",
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"upload_status": "validated"
},
{
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"accession": "IGVFFI4653RFBA",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR1_Rep1_S140"
],
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"creation_timestamp": "2024-06-11T20:51:33.275649+00:00",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2502UDBL/",
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"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR3_Rep1_S152"
],
"content_type": "reads",
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"file_format": "fastq",
"file_size": 24721617,
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"s3_uri": "s3://igvf-files/2024/06/01/d7bee24e-3fd0-4ffb-8d9b-4dcd3dc0cdc6/IGVFFI2502UDBL.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4385VBWZ/",
"accession": "IGVFFI4385VBWZ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR4_Rep2_S213"
],
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2568FNBM/",
"accession": "IGVFFI2568FNBM",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR3_Rep1_S152"
],
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"file_format": "yaml",
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"href": "/configuration-files/IGVFFI2568FNBM/@@download/IGVFFI2568FNBM.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/88b9c789-6255-4fb9-b852-f225418408ad/IGVFFI2568FNBM.yaml.gz",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9220ZDKH/",
"accession": "IGVFFI9220ZDKH",
"aliases": [
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],
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2148WQLI/",
"accession": "IGVFFI2148WQLI",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR2_Rep1_S146"
],
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6947RKEO/",
"accession": "IGVFFI6947RKEO",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR1_Rep2_S195"
],
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9861RLTL/",
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],
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6772UIRN/",
"accession": "IGVFFI6772UIRN",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR2_Rep2_S201"
],
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4207NYCN/",
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"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR4_Rep1_S158"
],
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0457OIVE/",
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"aliases": [
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],
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"href": "/configuration-files/IGVFFI0457OIVE/@@download/IGVFFI0457OIVE.yaml.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3737AKUY/",
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],
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},
{
"@id": "/configuration-files/IGVFFI4158BVCP/",
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],
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"href": "/configuration-files/IGVFFI4158BVCP/@@download/IGVFFI4158BVCP.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/65b91d6d-dbfc-45ed-9f02-31d84cc4e6d7/IGVFFI4158BVCP.yaml.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1727DFOC/",
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],
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5460AWQH/",
"accession": "IGVFFI5460AWQH",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR4_Rep2_S213"
],
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"href": "/configuration-files/IGVFFI5460AWQH/@@download/IGVFFI5460AWQH.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/899ce2cf-7678-4489-a6ab-22cf1ba65188/IGVFFI5460AWQH.yaml.gz",
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"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS1564ZVKC/",
"accession": "IGVFDS1564ZVKC",
"aliases": [
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR1_Rep1_S140",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR1_Rep2_S195",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR2_Rep1_S146",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR2_Rep2_S201",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR3_Rep1_S152",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR3_Rep2_S207",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR4_Rep1_S158",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR4_Rep2_S213"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:22:11.455194+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3012RMVA/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3012RMVA",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR1_Rep1_S140",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR1_Rep2_S195",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR2_Rep1_S146",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR2_Rep2_S201",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR3_Rep1_S152",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR3_Rep2_S207",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR4_Rep1_S158",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR4_Rep2_S213"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS7857SYCK/"
],
"modifications": [
"/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/",
"/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/"
],
"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 F for 80-100% expression of MYC) treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours, modified with a guide library",
"taxa": "Homo sapiens",
"treatments": [
"/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/"
]
}
],
"schema_version": "11",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-01T02:06:31.321958+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "3b7612d2-03fb-4de5-b0e9-f03548a5c7eb"
}