{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS0973WJFG/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS0973WJFG",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF2-BinA-PCR1-Rep1_S13",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF2-BinA-PCR2-Rep1_S19",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF2-BinA-PCR3-Rep1_S67",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF2-BinA-PCR4-Rep1_S73"
],
"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 [IGVFDS0973WJFG](/auxiliary-sets/IGVFDS0973WJFG/) has sequence file(s) [IGVFFI6243FYBR](/sequence-files/IGVFFI6243FYBR/), [IGVFFI7019VFXA](/sequence-files/IGVFFI7019VFXA/), [IGVFFI6771EVQT](/sequence-files/IGVFFI6771EVQT/), [IGVFFI4247GQHT](/sequence-files/IGVFFI4247GQHT/) 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/IGVFDS0973WJFG/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS0973WJFG](/auxiliary-sets/IGVFDS0973WJFG/) 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/IGVFDS0973WJFG/"
}
]
},
"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": "2024-05-14T20:31:16.766762+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",
"files": [
{
"@id": "/sequence-files/IGVFFI6243FYBR/",
"accession": "IGVFFI6243FYBR",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF2-BinA-PCR1-Rep1_S13"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:45:48.209884+00:00",
"file_format": "fastq",
"file_size": 6177567,
"href": "/sequence-files/IGVFFI6243FYBR/@@download/IGVFFI6243FYBR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/adaf0d1d-264d-45b4-ae66-6b73fdc6febf/IGVFFI6243FYBR.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin0hrs-FF2-BinA-PCR1-Rep1_S13_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2857WQAX/",
"accession": "IGVFFI2857WQAX",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF2-BinA-PCR1-Rep1_S13"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:38:17.678375+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI2857WQAX/@@download/IGVFFI2857WQAX.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/3eca1820-807d-486d-a2d8-d70c2371d3e7/IGVFFI2857WQAX.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF2-BinA-PCR1-Rep1_S13.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7019VFXA/",
"accession": "IGVFFI7019VFXA",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF2-BinA-PCR3-Rep1_S67"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:46:28.970930+00:00",
"file_format": "fastq",
"file_size": 9328708,
"href": "/sequence-files/IGVFFI7019VFXA/@@download/IGVFFI7019VFXA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/f13e8558-9e10-40f9-9746-bc1e27f45f4c/IGVFFI7019VFXA.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin0hrs-FF2-BinA-PCR3-Rep1_S67_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6771EVQT/",
"accession": "IGVFFI6771EVQT",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF2-BinA-PCR2-Rep1_S19"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:46:09.859329+00:00",
"file_format": "fastq",
"file_size": 4952264,
"href": "/sequence-files/IGVFFI6771EVQT/@@download/IGVFFI6771EVQT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/c3f9ca68-3eab-4570-aa84-28a1609ecd93/IGVFFI6771EVQT.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin0hrs-FF2-BinA-PCR2-Rep1_S19_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4441EASD/",
"accession": "IGVFFI4441EASD",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF2-BinA-PCR4-Rep1_S73"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:39:27.359494+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI4441EASD/@@download/IGVFFI4441EASD.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/dc3fa148-7d9d-4ba6-a511-13bdf45930c2/IGVFFI4441EASD.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF2-BinA-PCR4-Rep1_S73.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4247GQHT/",
"accession": "IGVFFI4247GQHT",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF2-BinA-PCR4-Rep1_S73"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:46:46.856618+00:00",
"file_format": "fastq",
"file_size": 9874636,
"href": "/sequence-files/IGVFFI4247GQHT/@@download/IGVFFI4247GQHT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/396d8baa-a821-4b54-ad71-206a5c8aa057/IGVFFI4247GQHT.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin0hrs-FF2-BinA-PCR4-Rep1_S73_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6027ZNLE/",
"accession": "IGVFFI6027ZNLE",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF2-BinA-PCR2-Rep1_S19"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:38:33.207500+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI6027ZNLE/@@download/IGVFFI6027ZNLE.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/9d6acb58-c486-4abd-9497-f2f499d94c4f/IGVFFI6027ZNLE.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF2-BinA-PCR2-Rep1_S19.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1495ZCSS/",
"accession": "IGVFFI1495ZCSS",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF2-BinA-PCR3-Rep1_S67"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:39:11.703997+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI1495ZCSS/@@download/IGVFFI1495ZCSS.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/98d7dd10-a46e-4746-aec9-6519da3b8de6/IGVFFI1495ZCSS.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF2-BinA-PCR3-Rep1_S67.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS9987GPMG/",
"accession": "IGVFDS9987GPMG",
"aliases": [
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF2-BinA-PCR1-Rep1_S13",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF2-BinA-PCR2-Rep1_S19",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF2-BinA-PCR3-Rep1_S67",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF2-BinA-PCR4-Rep1_S73"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:24:25.518485+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1725FTKZ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1725FTKZ",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF2-BinA-PCR1-Rep1_S13",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF2-BinA-PCR2-Rep1_S19",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF2-BinA-PCR3-Rep1_S67",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF2-BinA-PCR4-Rep1_S73"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS5413RKIA/"
],
"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 A for 0-10% expression of SSFA2) 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": "2024-06-01T01:45:48.209884+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "566f30cf-8de2-4a65-91d3-97f4b7d06ad1"
}