{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS0426GXQB/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS0426GXQB",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF2-BinF-PCR1_S18",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF2-BinF-PCR2_S24",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF2-BinF-PCR3_S114",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF2-BinF-PCR4_S120"
],
"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 [IGVFDS0426GXQB](/auxiliary-sets/IGVFDS0426GXQB/) has sequence file(s) [IGVFFI3207TTVR](/sequence-files/IGVFFI3207TTVR/), [IGVFFI5488NRJE](/sequence-files/IGVFFI5488NRJE/), [IGVFFI4644CRZB](/sequence-files/IGVFFI4644CRZB/), [IGVFFI4200EWKJ](/sequence-files/IGVFFI4200EWKJ/) 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/IGVFDS0426GXQB/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS0426GXQB](/auxiliary-sets/IGVFDS0426GXQB/) 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/IGVFDS0426GXQB/"
}
]
},
"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": "2024-05-16T17:41:33.743883+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/IGVFFI3207TTVR/",
"accession": "IGVFFI3207TTVR",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF2-BinF-PCR1_S18"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:14:44.348505+00:00",
"file_format": "fastq",
"file_size": 11348763,
"href": "/sequence-files/IGVFFI3207TTVR/@@download/IGVFFI3207TTVR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/f3426c18-3772-445d-9f19-4c263f1190d4/IGVFFI3207TTVR.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF2-BinF-PCR1_S18_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1929STRW/",
"accession": "IGVFFI1929STRW",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF2-BinF-PCR1_S18"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:06:46.414136+00:00",
"file_format": "yaml",
"file_size": 900,
"href": "/configuration-files/IGVFFI1929STRW/@@download/IGVFFI1929STRW.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/4f759968-432a-4482-b9b1-145e91ce4991/IGVFFI1929STRW.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF2-BinF-PCR1_S18.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5488NRJE/",
"accession": "IGVFFI5488NRJE",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF2-BinF-PCR2_S24"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:15:02.033147+00:00",
"file_format": "fastq",
"file_size": 15233292,
"href": "/sequence-files/IGVFFI5488NRJE/@@download/IGVFFI5488NRJE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/26beaf4b-b9bb-459b-ab6c-bc1bad3994cb/IGVFFI5488NRJE.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF2-BinF-PCR2_S24_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4786CMQR/",
"accession": "IGVFFI4786CMQR",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF2-BinF-PCR2_S24"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:06:59.996074+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI4786CMQR/@@download/IGVFFI4786CMQR.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/2214d1e5-d296-4952-93f1-5f64aaa282d6/IGVFFI4786CMQR.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF2-BinF-PCR2_S24.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4644CRZB/",
"accession": "IGVFFI4644CRZB",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF2-BinF-PCR3_S114"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:17:04.257822+00:00",
"file_format": "fastq",
"file_size": 22488401,
"href": "/sequence-files/IGVFFI4644CRZB/@@download/IGVFFI4644CRZB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/158fd8ac-6a3d-4bb3-8649-9dc6a961094e/IGVFFI4644CRZB.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF2-BinF-PCR3_S114_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4200EWKJ/",
"accession": "IGVFFI4200EWKJ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF2-BinF-PCR4_S120"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:17:22.028765+00:00",
"file_format": "fastq",
"file_size": 30569605,
"href": "/sequence-files/IGVFFI4200EWKJ/@@download/IGVFFI4200EWKJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/db5f83ec-218f-436b-8528-fb9a4f1b32dc/IGVFFI4200EWKJ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF2-BinF-PCR4_S120_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9179ZFTQ/",
"accession": "IGVFFI9179ZFTQ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF2-BinF-PCR3_S114"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:07:13.393591+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI9179ZFTQ/@@download/IGVFFI9179ZFTQ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/30a3219f-86d1-4f63-86df-542f7ec19925/IGVFFI9179ZFTQ.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF2-BinF-PCR3_S114.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4146MVTA/",
"accession": "IGVFFI4146MVTA",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF2-BinF-PCR4_S120"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:07:26.708785+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI4146MVTA/@@download/IGVFFI4146MVTA.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/147ad493-d576-4142-b6f1-bf6ff52ddc43/IGVFFI4146MVTA.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF2-BinF-PCR4_S120.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS4623YYCA/",
"accession": "IGVFDS4623YYCA",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinF-PCR1_S18",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinF-PCR2_S24",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinF-PCR3_S114",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinF-PCR4_S120"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:14:50.075674+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1737WNTH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1737WNTH",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinF-PCR1_S18",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinF-PCR2_S24",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinF-PCR3_S114",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinF-PCR4_S120"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS7846UISG/"
],
"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 F for 80-100% expression of KITLG) 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": "2024-06-01T02:14:44.348505+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "d7b6f9f6-eb4c-4ac0-b118-108bb731bd8e"
}