{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS2059NFJA/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS2059NFJA",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinE-PCR1_Rep1_S29",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinE-PCR1_Rep2_S84",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinE-PCR2_Rep1_S35",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinE-PCR2_Rep2_S90",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinE-PCR3_Rep1_S41",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinE-PCR3_Rep2_S96",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinE-PCR4_Rep1_S47",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinE-PCR4_Rep2_S102"
],
"audit": {
"INTERNAL_ACTION": [
{
"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 [IGVFDS2059NFJA](/auxiliary-sets/IGVFDS2059NFJA/) has sequence file(s) [IGVFFI4334TLKF](/sequence-files/IGVFFI4334TLKF/), [IGVFFI8214NGYS](/sequence-files/IGVFFI8214NGYS/), [IGVFFI2421MJBY](/sequence-files/IGVFFI2421MJBY/), [IGVFFI0157HGQY](/sequence-files/IGVFFI0157HGQY/), [IGVFFI6105CYOK](/sequence-files/IGVFFI6105CYOK/), [IGVFFI2543THHO](/sequence-files/IGVFFI2543THHO/), [IGVFFI2477AUWQ](/sequence-files/IGVFFI2477AUWQ/), [IGVFFI1421XINF](/sequence-files/IGVFFI1421XINF/) 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/IGVFDS2059NFJA/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS2059NFJA](/auxiliary-sets/IGVFDS2059NFJA/) 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/IGVFDS2059NFJA/"
}
]
},
"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": "2024-05-21T17:13:09.675768+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",
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{
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"accession": "IGVFFI4334TLKF",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinE-PCR1_Rep1_S29"
],
"content_type": "reads",
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"file_format": "fastq",
"file_size": 36825085,
"href": "/sequence-files/IGVFFI4334TLKF/@@download/IGVFFI4334TLKF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/a7d23454-e9c5-4732-994f-9aa05969c03a/IGVFFI4334TLKF.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1277NHCZ/",
"accession": "IGVFFI1277NHCZ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinE-PCR1_Rep1_S29"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:47:34.760382+00:00",
"file_format": "yaml",
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"href": "/configuration-files/IGVFFI1277NHCZ/@@download/IGVFFI1277NHCZ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/fe4addec-009f-4b82-ac2e-c9b481a9b291/IGVFFI1277NHCZ.yaml.gz",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8214NGYS/",
"accession": "IGVFFI8214NGYS",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinE-PCR3_Rep2_S96"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:02:45.468389+00:00",
"file_format": "fastq",
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"href": "/sequence-files/IGVFFI8214NGYS/@@download/IGVFFI8214NGYS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/49f1923d-1e0a-4fba-b8d3-8839b89bf3b3/IGVFFI8214NGYS.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF2-BinE-PCR3-Rep2_S96_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2421MJBY/",
"accession": "IGVFFI2421MJBY",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinE-PCR4_Rep1_S47"
],
"content_type": "reads",
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"file_size": 48725143,
"href": "/sequence-files/IGVFFI2421MJBY/@@download/IGVFFI2421MJBY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/1e65b563-1498-44b0-942f-056887aa5571/IGVFFI2421MJBY.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF2-BinE-PCR4-Rep1_S47_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0157HGQY/",
"accession": "IGVFFI0157HGQY",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinE-PCR2_Rep2_S90"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:02:04.606294+00:00",
"file_format": "fastq",
"file_size": 19770986,
"href": "/sequence-files/IGVFFI0157HGQY/@@download/IGVFFI0157HGQY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/1362bf34-70e2-4f6e-b52c-bfe4837b15fb/IGVFFI0157HGQY.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF2-BinE-PCR2-Rep2_S90_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9101BJPA/",
"accession": "IGVFFI9101BJPA",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinE-PCR1_Rep2_S84"
],
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"href": "/configuration-files/IGVFFI9101BJPA/@@download/IGVFFI9101BJPA.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/ad0fe47a-e577-4110-a7b8-3ab6fb4d8399/IGVFFI9101BJPA.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF2-BinE-PCR1_Rep2_S84.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6105CYOK/",
"accession": "IGVFFI6105CYOK",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinE-PCR1_Rep2_S84"
],
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"href": "/sequence-files/IGVFFI6105CYOK/@@download/IGVFFI6105CYOK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/8cd4152b-224e-43ac-9341-90bf8b96cddc/IGVFFI6105CYOK.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2543THHO/",
"accession": "IGVFFI2543THHO",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinE-PCR2_Rep1_S35"
],
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2477AUWQ/",
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],
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8666DAFD/",
"accession": "IGVFFI8666DAFD",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinE-PCR2_Rep1_S35"
],
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1421XINF/",
"accession": "IGVFFI1421XINF",
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],
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},
{
"@id": "/configuration-files/IGVFFI8039VKQB/",
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],
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5984EMJS/",
"accession": "IGVFFI5984EMJS",
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],
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7487YMTW/",
"accession": "IGVFFI7487YMTW",
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],
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"href": "/configuration-files/IGVFFI7487YMTW/@@download/IGVFFI7487YMTW.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/4919bccb-eeff-4a89-9e1b-b98a47cbcd75/IGVFFI7487YMTW.yaml.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4591ZSAY/",
"accession": "IGVFFI4591ZSAY",
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],
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2198DRUQ/",
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"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinE-PCR4_Rep2_S102"
],
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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/IGVFDS5847JIJX/",
"accession": "IGVFDS5847JIJX",
"aliases": [
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinE-PCR1_Rep1_S29",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinE-PCR1_Rep2_S84",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinE-PCR2_Rep1_S35",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinE-PCR2_Rep2_S90",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinE-PCR3_Rep1_S41",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinE-PCR3_Rep2_S96",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinE-PCR4_Rep1_S47",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinE-PCR4_Rep2_S102"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:20:31.161876+00:00",
"samples": [
{
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"@type": [
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"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1124JJAA",
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"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinE-PCR1_Rep2_S84",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinE-PCR2_Rep1_S35",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinE-PCR2_Rep2_S90",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinE-PCR3_Rep1_S41",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinE-PCR3_Rep2_S96",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinE-PCR4_Rep1_S47",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinE-PCR4_Rep2_S102"
],
"classifications": [
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],
"construct_library_sets": [
"/construct-library-sets/IGVFDS7857SYCK/"
],
"modifications": [
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],
"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) modified 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": "2024-06-01T02:00:58.432177+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "c1ffa179-8909-4821-8e4b-9989556c2e0f"
}