{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS4010VNGF/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS4010VNGF",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR1-Rep1_S122",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR2-Rep1_S128",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR3-Rep1_S176",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR4-Rep1_S182"
],
"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 [IGVFDS4010VNGF](/auxiliary-sets/IGVFDS4010VNGF/) has sequence file(s) [IGVFFI4161WIYC](/sequence-files/IGVFFI4161WIYC/), [IGVFFI5330ZBZF](/sequence-files/IGVFFI5330ZBZF/), [IGVFFI6786VTNX](/sequence-files/IGVFFI6786VTNX/), [IGVFFI0237YEQF](/sequence-files/IGVFFI0237YEQF/) 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/IGVFDS4010VNGF/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS4010VNGF](/auxiliary-sets/IGVFDS4010VNGF/) 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/IGVFDS4010VNGF/"
}
]
},
"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": "2024-05-14T16:24:19.367918+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/IGVFFI4161WIYC/",
"accession": "IGVFFI4161WIYC",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR1-Rep1_S122"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:52:09.910992+00:00",
"file_format": "fastq",
"file_size": 15031923,
"href": "/sequence-files/IGVFFI4161WIYC/@@download/IGVFFI4161WIYC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/a3a66435-bad2-4ea4-b510-e3a7709e76a4/IGVFFI4161WIYC.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/FAM3C-Auxin0hrs-FF2-BinB-PCR1-Rep1_S122_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8739NONQ/",
"accession": "IGVFFI8739NONQ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR1-Rep1_S122"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:42:48.825129+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI8739NONQ/@@download/IGVFFI8739NONQ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/7595ec06-0f54-482c-b261-4e4b14f7e418/IGVFFI8739NONQ.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF2-BinB-PCR1-Rep1_S122.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5330ZBZF/",
"accession": "IGVFFI5330ZBZF",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR2-Rep1_S128"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:52:28.220317+00:00",
"file_format": "fastq",
"file_size": 13261753,
"href": "/sequence-files/IGVFFI5330ZBZF/@@download/IGVFFI5330ZBZF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/eb458fc3-1f12-4329-b7b5-59f39c61c0e8/IGVFFI5330ZBZF.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/FAM3C-Auxin0hrs-FF2-BinB-PCR2-Rep1_S128_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6786VTNX/",
"accession": "IGVFFI6786VTNX",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR3-Rep1_S176"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:52:46.255837+00:00",
"file_format": "fastq",
"file_size": 25060691,
"href": "/sequence-files/IGVFFI6786VTNX/@@download/IGVFFI6786VTNX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/e342dd20-bb98-4939-9231-6fb3157dd5a0/IGVFFI6786VTNX.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/FAM3C-Auxin0hrs-FF2-BinB-PCR3-Rep1_S176_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0237YEQF/",
"accession": "IGVFFI0237YEQF",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR4-Rep1_S182"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:53:04.498696+00:00",
"file_format": "fastq",
"file_size": 22293288,
"href": "/sequence-files/IGVFFI0237YEQF/@@download/IGVFFI0237YEQF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/4793a8ad-18c3-4cac-8b3e-56c405d82d32/IGVFFI0237YEQF.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/FAM3C-Auxin0hrs-FF2-BinB-PCR4-Rep1_S182_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3135DSDD/",
"accession": "IGVFFI3135DSDD",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR4-Rep1_S182"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:43:29.934271+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI3135DSDD/@@download/IGVFFI3135DSDD.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/0388b421-978f-4f84-8334-ad3fe4bad3ff/IGVFFI3135DSDD.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF2-BinB-PCR4-Rep1_S182.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2775UGHY/",
"accession": "IGVFFI2775UGHY",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR2-Rep1_S128"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:43:02.488282+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI2775UGHY/@@download/IGVFFI2775UGHY.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/36624d58-64f2-4f30-b001-49115769d501/IGVFFI2775UGHY.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF2-BinB-PCR2-Rep1_S128.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5430OQAY/",
"accession": "IGVFFI5430OQAY",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR3-Rep1_S176"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:43:16.719372+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI5430OQAY/@@download/IGVFFI5430OQAY.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/09445a76-3b78-40eb-be23-6ea949669e94/IGVFFI5430OQAY.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF2-BinB-PCR3-Rep1_S176.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS6663FDTV/",
"accession": "IGVFDS6663FDTV",
"aliases": [
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR1-Rep1_S122",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR2-Rep1_S128",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR3-Rep1_S176",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR4-Rep1_S182"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:11:29.314895+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3569TFCR/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3569TFCR",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR1-Rep1_S122",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR2-Rep1_S128",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR3-Rep1_S176",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR4-Rep1_S182"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS1891GTLU/"
],
"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 FAM3C) 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": "2024-06-01T01:52:09.910992+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "e2c5af2d-b057-4f9c-89f7-a292eb43a8a3"
}