{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS6371DGFM/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS6371DGFM",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF2-BinB-PCR1-Rep1_S14",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF2-BinB-PCR2-Rep1_S20",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF2-BinB-PCR3-Rep1_S68",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF2-BinB-PCR4-Rep1_S74"
],
"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 [IGVFDS6371DGFM](/auxiliary-sets/IGVFDS6371DGFM/) has sequence file(s) [IGVFFI5491PJJA](/sequence-files/IGVFFI5491PJJA/), [IGVFFI4362WDJQ](/sequence-files/IGVFFI4362WDJQ/), [IGVFFI5725FLXU](/sequence-files/IGVFFI5725FLXU/), [IGVFFI2184WUSE](/sequence-files/IGVFFI2184WUSE/) 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/IGVFDS6371DGFM/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS6371DGFM](/auxiliary-sets/IGVFDS6371DGFM/) 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/IGVFDS6371DGFM/"
}
]
},
"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": "2024-05-14T20:31:17.647649+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/IGVFFI5491PJJA/",
"accession": "IGVFFI5491PJJA",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF2-BinB-PCR1-Rep1_S14"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:45:50.947420+00:00",
"file_format": "fastq",
"file_size": 15935544,
"href": "/sequence-files/IGVFFI5491PJJA/@@download/IGVFFI5491PJJA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/5499c74d-8d27-47ff-8edd-1450dc9e90aa/IGVFFI5491PJJA.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-BinB-PCR1-Rep1_S14_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2363WMDW/",
"accession": "IGVFFI2363WMDW",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF2-BinB-PCR1-Rep1_S14"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:38:20.213547+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI2363WMDW/@@download/IGVFFI2363WMDW.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/12a0858f-a9f8-4ee7-9a34-f1b837c41563/IGVFFI2363WMDW.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF2-BinB-PCR1-Rep1_S14.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4362WDJQ/",
"accession": "IGVFFI4362WDJQ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF2-BinB-PCR3-Rep1_S68"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:46:31.905002+00:00",
"file_format": "fastq",
"file_size": 18232073,
"href": "/sequence-files/IGVFFI4362WDJQ/@@download/IGVFFI4362WDJQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/4cd67329-628b-4871-a093-6fb3b08565b6/IGVFFI4362WDJQ.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-BinB-PCR3-Rep1_S68_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5725FLXU/",
"accession": "IGVFFI5725FLXU",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF2-BinB-PCR4-Rep1_S74"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:46:49.751124+00:00",
"file_format": "fastq",
"file_size": 15289143,
"href": "/sequence-files/IGVFFI5725FLXU/@@download/IGVFFI5725FLXU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/500bec00-5b4e-4e86-b218-5b0a678e17c8/IGVFFI5725FLXU.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-BinB-PCR4-Rep1_S74_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2184WUSE/",
"accession": "IGVFFI2184WUSE",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF2-BinB-PCR2-Rep1_S20"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:46:12.763401+00:00",
"file_format": "fastq",
"file_size": 9313356,
"href": "/sequence-files/IGVFFI2184WUSE/@@download/IGVFFI2184WUSE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/4018eaa8-000d-4f03-8d83-62ae448395cc/IGVFFI2184WUSE.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-BinB-PCR2-Rep1_S20_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5482EMRY/",
"accession": "IGVFFI5482EMRY",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF2-BinB-PCR3-Rep1_S68"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:39:14.148400+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI5482EMRY/@@download/IGVFFI5482EMRY.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/8073cbdc-6fe5-4448-be57-883c314efd49/IGVFFI5482EMRY.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF2-BinB-PCR3-Rep1_S68.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5818VALN/",
"accession": "IGVFFI5818VALN",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF2-BinB-PCR2-Rep1_S20"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:38:35.692742+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI5818VALN/@@download/IGVFFI5818VALN.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/ab71d207-eacf-44b3-9dff-a3f53ce72afe/IGVFFI5818VALN.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF2-BinB-PCR2-Rep1_S20.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7087XIZI/",
"accession": "IGVFFI7087XIZI",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF2-BinB-PCR4-Rep1_S74"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:39:29.923381+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI7087XIZI/@@download/IGVFFI7087XIZI.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/72a9dd7d-8d93-4397-bdd3-9aec6864ec51/IGVFFI7087XIZI.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF2-BinB-PCR4-Rep1_S74.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS9546RHPY/",
"accession": "IGVFDS9546RHPY",
"aliases": [
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF2-BinB-PCR1-Rep1_S14",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF2-BinB-PCR2-Rep1_S20",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF2-BinB-PCR3-Rep1_S68",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF2-BinB-PCR4-Rep1_S74"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:24:32.738289+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9860IGWK/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9860IGWK",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF2-BinB-PCR1-Rep1_S14",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF2-BinB-PCR2-Rep1_S20",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF2-BinB-PCR3-Rep1_S68",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF2-BinB-PCR4-Rep1_S74"
],
"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 B for 10-20% 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": "2024-06-01T01:45:50.947420+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "9b93825e-01ae-42c3-b1cd-a01a9c6e0a09"
}