{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS7753HONE/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS7753HONE",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF2-BinE-PCR1_S17",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF2-BinE-PCR2_S23",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF2-BinE-PCR3_S113",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF2-BinE-PCR4_S119"
],
"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 [IGVFDS7753HONE](/auxiliary-sets/IGVFDS7753HONE/) has sequence file(s) [IGVFFI6004KUNG](/sequence-files/IGVFFI6004KUNG/), [IGVFFI4888REEW](/sequence-files/IGVFFI4888REEW/), [IGVFFI4302EURY](/sequence-files/IGVFFI4302EURY/), [IGVFFI7967STOK](/sequence-files/IGVFFI7967STOK/) 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/IGVFDS7753HONE/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS7753HONE](/auxiliary-sets/IGVFDS7753HONE/) 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/IGVFDS7753HONE/"
}
]
},
"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": "2024-05-16T17:41:32.612056+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/IGVFFI6004KUNG/",
"accession": "IGVFFI6004KUNG",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF2-BinE-PCR1_S17"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:14:41.760588+00:00",
"file_format": "fastq",
"file_size": 2872205,
"href": "/sequence-files/IGVFFI6004KUNG/@@download/IGVFFI6004KUNG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/8f9fd099-3ad8-40cb-b90c-0e0a6895e9b1/IGVFFI6004KUNG.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF2-BinE-PCR1_S17_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3756GQZG/",
"accession": "IGVFFI3756GQZG",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF2-BinE-PCR1_S17"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:06:44.114700+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI3756GQZG/@@download/IGVFFI3756GQZG.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/7007c891-0fb3-490e-b65d-93c6ac0a4490/IGVFFI3756GQZG.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF2-BinE-PCR1_S17.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4888REEW/",
"accession": "IGVFFI4888REEW",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF2-BinE-PCR4_S119"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:17:19.211616+00:00",
"file_format": "fastq",
"file_size": 16205238,
"href": "/sequence-files/IGVFFI4888REEW/@@download/IGVFFI4888REEW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/d2527f18-21cd-400a-a556-6088ed44fd7e/IGVFFI4888REEW.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF2-BinE-PCR4_S119_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6848VWFJ/",
"accession": "IGVFFI6848VWFJ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF2-BinE-PCR2_S23"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:06:57.740616+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI6848VWFJ/@@download/IGVFFI6848VWFJ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/6900f5d2-bf26-4f71-81b3-15a8fa3b081c/IGVFFI6848VWFJ.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF2-BinE-PCR2_S23.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4302EURY/",
"accession": "IGVFFI4302EURY",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF2-BinE-PCR2_S23"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:14:59.272481+00:00",
"file_format": "fastq",
"file_size": 7422037,
"href": "/sequence-files/IGVFFI4302EURY/@@download/IGVFFI4302EURY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/8a05be0b-8807-40b2-a306-46e2bba950dc/IGVFFI4302EURY.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF2-BinE-PCR2_S23_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7967STOK/",
"accession": "IGVFFI7967STOK",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF2-BinE-PCR3_S113"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:17:01.141538+00:00",
"file_format": "fastq",
"file_size": 11451670,
"href": "/sequence-files/IGVFFI7967STOK/@@download/IGVFFI7967STOK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/ae17dcb3-ba2e-4f80-9f73-5ed95b8e18c8/IGVFFI7967STOK.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF2-BinE-PCR3_S113_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3445KTGV/",
"accession": "IGVFFI3445KTGV",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF2-BinE-PCR4_S119"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:07:24.525471+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI3445KTGV/@@download/IGVFFI3445KTGV.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/e8f48e4c-6ff5-4bff-a426-790c7e3f6bf0/IGVFFI3445KTGV.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF2-BinE-PCR4_S119.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8709FCAZ/",
"accession": "IGVFFI8709FCAZ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF2-BinE-PCR3_S113"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:07:11.250180+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI8709FCAZ/@@download/IGVFFI8709FCAZ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/6b5f57d8-0176-4150-a2ff-145b5ebbf07a/IGVFFI8709FCAZ.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF2-BinE-PCR3_S113.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS8133FFMV/",
"accession": "IGVFDS8133FFMV",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinE-PCR1_S17",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinE-PCR2_S23",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinE-PCR3_S113",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinE-PCR4_S119"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:14:42.667983+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9074NPMT/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9074NPMT",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinE-PCR1_S17",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinE-PCR2_S23",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinE-PCR3_S113",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinE-PCR4_S119"
],
"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 E for 80-90% 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": "2024-06-01T02:14:41.760588+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "975c4ee3-ffed-461f-968e-f614591cecda"
}