{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS9738NANI/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS9738NANI",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR1_Rep1_S25",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR1_Rep2_S80",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR2_Rep1_S31",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR2_Rep2_S86",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR3_Rep1_S37",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR3_Rep2_S92",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR4_Rep1_S43",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR4_Rep2_S98"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS9738NANI](/auxiliary-sets/IGVFDS9738NANI/) has sequence file(s) [IGVFFI0450VGJL](/sequence-files/IGVFFI0450VGJL/), [IGVFFI4364CKDK](/sequence-files/IGVFFI4364CKDK/), [IGVFFI6307WYZS](/sequence-files/IGVFFI6307WYZS/), [IGVFFI0700SJDG](/sequence-files/IGVFFI0700SJDG/), [IGVFFI0269PZHU](/sequence-files/IGVFFI0269PZHU/), [IGVFFI2787YXFO](/sequence-files/IGVFFI2787YXFO/), [IGVFFI3163PWLN](/sequence-files/IGVFFI3163PWLN/), [IGVFFI3236SBJX](/sequence-files/IGVFFI3236SBJX/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS9738NANI/"
}
]
},
"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": "2024-05-21T17:13:05.953865+00:00",
"donors": [
{
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"accession": "IGVFDO0384OZRW",
"aliases": [
"igvf:donor_of_HCT116"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
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{
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"accession": "IGVFFI0450VGJL",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR1_Rep1_S25"
],
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"creation_timestamp": "2024-06-01T02:00:44.627135+00:00",
"file_format": "fastq",
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"href": "/sequence-files/IGVFFI0450VGJL/@@download/IGVFFI0450VGJL.fastq.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8320WTKY/",
"accession": "IGVFFI8320WTKY",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR1_Rep1_S25"
],
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"href": "/configuration-files/IGVFFI8320WTKY/@@download/IGVFFI8320WTKY.yaml.gz",
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"status": "released",
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"upload_status": "validated"
},
{
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"accession": "IGVFFI4364CKDK",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR1_Rep2_S80"
],
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"file_format": "fastq",
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"sequencing_platform": "/platform-terms/EFO_0008565/",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6307WYZS/",
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"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR2_Rep1_S31"
],
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"creation_timestamp": "2024-06-01T02:01:25.917425+00:00",
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"file_size": 47247911,
"href": "/sequence-files/IGVFFI6307WYZS/@@download/IGVFFI6307WYZS.fastq.gz",
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"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0700SJDG/",
"accession": "IGVFFI0700SJDG",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR4_Rep1_S43"
],
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"creation_timestamp": "2024-06-01T02:02:52.921577+00:00",
"file_format": "fastq",
"file_size": 34358898,
"href": "/sequence-files/IGVFFI0700SJDG/@@download/IGVFFI0700SJDG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/aab548e2-6b82-4e91-a6d5-c750ebd8a571/IGVFFI0700SJDG.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0269PZHU/",
"accession": "IGVFFI0269PZHU",
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],
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"creation_timestamp": "2024-06-01T02:02:11.613420+00:00",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2787YXFO/",
"accession": "IGVFFI2787YXFO",
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],
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"creation_timestamp": "2024-06-01T02:01:50.554640+00:00",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3163PWLN/",
"accession": "IGVFFI3163PWLN",
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"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR4_Rep2_S98"
],
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3236SBJX/",
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],
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9283MPSI/",
"accession": "IGVFFI9283MPSI",
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],
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1697OBKN/",
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],
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6808FPSN/",
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],
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},
{
"@id": "/configuration-files/IGVFFI1710IDES/",
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"aliases": [
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],
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4380QFIT/",
"accession": "IGVFFI4380QFIT",
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"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR1_Rep2_S80"
],
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"href": "/configuration-files/IGVFFI4380QFIT/@@download/IGVFFI4380QFIT.yaml.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3170BIJY/",
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"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR3_Rep2_S92"
],
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7979CDQA/",
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"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR4_Rep2_S98"
],
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"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4544YEQM/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS3856ZADL/",
"accession": "IGVFDS3856ZADL",
"aliases": [
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR1_Rep1_S25",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR1_Rep2_S80",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR2_Rep1_S31",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR2_Rep2_S86",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR3_Rep1_S37",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR3_Rep2_S92",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR4_Rep1_S43",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR4_Rep2_S98"
],
"preferred_assay_title": "CRISPR FlowFISH screen",
"status": "released"
}
],
"release_timestamp": "2024-07-10T20:19:57.891711+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM6871QVFB/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6871QVFB",
"aliases": [
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"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR1_Rep2_S80",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR2_Rep1_S31",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR2_Rep2_S86",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR3_Rep1_S37",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR3_Rep2_S92",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR4_Rep1_S43",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR4_Rep2_S98"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS7857SYCK/"
],
"modifications": [
{
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},
{
"@id": "/degron-modifications/2e8d10cc-fc98-44d5-a7d9-e2892e16c98a/",
"modality": "degradation",
"status": "released"
}
],
"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 A for 0-10% expression of MYC) modified with CRISPRi Sp-dCas9-KOX1-KRAB, inactive AID system targeting RAD21, transfected with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "12",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-01T02:00:44.627135+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "ea37e9fc-cb66-4736-9b8c-d94f39ff6795"
}