{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS2834VAYS/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS2834VAYS",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR1_Rep1_S26",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR1_Rep2_S81",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR2_Rep1_S32",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR2_Rep2_S87",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR3_Rep1_S38",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR3_Rep2_S93",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR4_Rep1_S44",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR4_Rep2_S99"
],
"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 [IGVFDS2834VAYS](/auxiliary-sets/IGVFDS2834VAYS/) has sequence file(s) [IGVFFI7807KLUU](/sequence-files/IGVFFI7807KLUU/), [IGVFFI3275WQZQ](/sequence-files/IGVFFI3275WQZQ/), [IGVFFI4298DZIN](/sequence-files/IGVFFI4298DZIN/), [IGVFFI2362LKOQ](/sequence-files/IGVFFI2362LKOQ/), [IGVFFI5870UCTK](/sequence-files/IGVFFI5870UCTK/), [IGVFFI1545RRLD](/sequence-files/IGVFFI1545RRLD/), [IGVFFI9245IPZR](/sequence-files/IGVFFI9245IPZR/), [IGVFFI9172PREQ](/sequence-files/IGVFFI9172PREQ/) 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/IGVFDS2834VAYS/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS2834VAYS](/auxiliary-sets/IGVFDS2834VAYS/) 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/IGVFDS2834VAYS/"
}
]
},
"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": "2024-05-21T17:13:07.300301+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": "IGVFFI7807KLUU",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR1_Rep1_S26"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:00:48.191718+00:00",
"file_format": "fastq",
"file_size": 52386666,
"href": "/sequence-files/IGVFFI7807KLUU/@@download/IGVFFI7807KLUU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/46576688-e224-4930-ad48-e405c210bbcb/IGVFFI7807KLUU.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF2-BinB-PCR1-Rep1_S26_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8168MZFJ/",
"accession": "IGVFFI8168MZFJ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR1_Rep1_S26"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:47:27.584218+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI8168MZFJ/@@download/IGVFFI8168MZFJ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/f7361e23-06bf-4c80-a098-2519c2603519/IGVFFI8168MZFJ.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF2-BinB-PCR1_Rep1_S26.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3275WQZQ/",
"accession": "IGVFFI3275WQZQ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR1_Rep2_S81"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:01:08.892229+00:00",
"file_format": "fastq",
"file_size": 28552104,
"href": "/sequence-files/IGVFFI3275WQZQ/@@download/IGVFFI3275WQZQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/ca9629bd-aead-4685-8c24-0d14830cf977/IGVFFI3275WQZQ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF2-BinB-PCR1-Rep2_S81_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4298DZIN/",
"accession": "IGVFFI4298DZIN",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR3_Rep1_S38"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:02:15.190391+00:00",
"file_format": "fastq",
"file_size": 34006187,
"href": "/sequence-files/IGVFFI4298DZIN/@@download/IGVFFI4298DZIN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/e695ffd0-0f68-4feb-92d3-b1770d15935a/IGVFFI4298DZIN.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF2-BinB-PCR3-Rep1_S38_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1435OZLL/",
"accession": "IGVFFI1435OZLL",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR4_Rep1_S44"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:48:53.703128+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI1435OZLL/@@download/IGVFFI1435OZLL.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/bfbaf361-d9ac-41f6-9aba-99cccb7bea21/IGVFFI1435OZLL.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF2-BinB-PCR4_Rep1_S44.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2362LKOQ/",
"accession": "IGVFFI2362LKOQ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR4_Rep1_S44"
],
"content_type": "reads",
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"file_format": "fastq",
"file_size": 38235310,
"href": "/sequence-files/IGVFFI2362LKOQ/@@download/IGVFFI2362LKOQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/1bd71244-8bdc-447b-9b8a-a3c8995ee2a3/IGVFFI2362LKOQ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF2-BinB-PCR4-Rep1_S44_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7331TUOS/",
"accession": "IGVFFI7331TUOS",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR4_Rep2_S99"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:49:08.624866+00:00",
"file_format": "yaml",
"file_size": 910,
"href": "/configuration-files/IGVFFI7331TUOS/@@download/IGVFFI7331TUOS.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/3c79d8ce-69e9-44ce-9423-024c59b20fb3/IGVFFI7331TUOS.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF2-BinB-PCR4_Rep2_S99.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5870UCTK/",
"accession": "IGVFFI5870UCTK",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR2_Rep1_S32"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:01:33.300910+00:00",
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"href": "/sequence-files/IGVFFI5870UCTK/@@download/IGVFFI5870UCTK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/f75ed6e6-66d6-4fd7-b3a8-2c635f43d0ef/IGVFFI5870UCTK.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF2-BinB-PCR2-Rep1_S32_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1545RRLD/",
"accession": "IGVFFI1545RRLD",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR2_Rep2_S87"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:01:53.919516+00:00",
"file_format": "fastq",
"file_size": 28097455,
"href": "/sequence-files/IGVFFI1545RRLD/@@download/IGVFFI1545RRLD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/9b6c6ef0-bf75-42bf-bea0-3196f183148d/IGVFFI1545RRLD.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF2-BinB-PCR2-Rep2_S87_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9245IPZR/",
"accession": "IGVFFI9245IPZR",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR3_Rep2_S93"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:02:35.609914+00:00",
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"href": "/sequence-files/IGVFFI9245IPZR/@@download/IGVFFI9245IPZR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/8f5eab92-9563-45e0-8044-486283f62377/IGVFFI9245IPZR.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9172PREQ/",
"accession": "IGVFFI9172PREQ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR4_Rep2_S99"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:03:17.734658+00:00",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6802YWSU/",
"accession": "IGVFFI6802YWSU",
"aliases": [
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],
"content_type": "seqspec",
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"file_format": "yaml",
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"href": "/configuration-files/IGVFFI6802YWSU/@@download/IGVFFI6802YWSU.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/eac1decb-293f-417b-bd60-46d6423d7ac0/IGVFFI6802YWSU.yaml.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2068XJOM/",
"accession": "IGVFFI2068XJOM",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR2_Rep1_S32"
],
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"href": "/configuration-files/IGVFFI2068XJOM/@@download/IGVFFI2068XJOM.yaml.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2467IQLT/",
"accession": "IGVFFI2467IQLT",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR3_Rep2_S93"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:48:39.216286+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI2467IQLT/@@download/IGVFFI2467IQLT.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/d741966c-c596-49a2-b94c-97d7eb4808ac/IGVFFI2467IQLT.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF2-BinB-PCR3_Rep2_S93.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8314LAZS/",
"accession": "IGVFFI8314LAZS",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR2_Rep2_S87"
],
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"href": "/configuration-files/IGVFFI8314LAZS/@@download/IGVFFI8314LAZS.yaml.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2350VRGN/",
"accession": "IGVFFI2350VRGN",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR3_Rep1_S38"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:48:25.173512+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI2350VRGN/@@download/IGVFFI2350VRGN.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/b3e3988c-e110-4725-8b89-71b4fc31e943/IGVFFI2350VRGN.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF2-BinB-PCR3_Rep1_S38.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS0398KCYH/",
"accession": "IGVFDS0398KCYH",
"aliases": [
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR1_Rep1_S26",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR1_Rep2_S81",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR2_Rep1_S32",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR2_Rep2_S87",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR3_Rep1_S38",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR3_Rep2_S93",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR4_Rep1_S44",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR4_Rep2_S99"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:20:06.844779+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2313EONT/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2313EONT",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR1_Rep1_S26",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR1_Rep2_S81",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR2_Rep1_S32",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR2_Rep2_S87",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR3_Rep1_S38",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR3_Rep2_S93",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR4_Rep1_S44",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR4_Rep2_S99"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS7857SYCK/"
],
"modifications": [
"/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 B for 10-20% 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": "2024-06-01T02:00:48.191718+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "97595564-a0c8-4dc3-8969-0d92c2bfcee5"
}