{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS8765QBBH/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS8765QBBH",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF1-BinF-PCR1-Rep1_S114",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF1-BinF-PCR2-Rep1_S120",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF1-BinF-PCR3-Rep1_S168",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF1-BinF-PCR4-Rep1_S174"
],
"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 [IGVFDS8765QBBH](/auxiliary-sets/IGVFDS8765QBBH/) has sequence file(s) [IGVFFI2576YRDI](/sequence-files/IGVFFI2576YRDI/), [IGVFFI8149ZFKP](/sequence-files/IGVFFI8149ZFKP/), [IGVFFI4783GBNK](/sequence-files/IGVFFI4783GBNK/), [IGVFFI5568QDEG](/sequence-files/IGVFFI5568QDEG/) 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/IGVFDS8765QBBH/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS8765QBBH](/auxiliary-sets/IGVFDS8765QBBH/) 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/IGVFDS8765QBBH/"
}
]
},
"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": "2024-05-14T16:23:56.379110+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/IGVFFI2576YRDI/",
"accession": "IGVFFI2576YRDI",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF1-BinF-PCR1-Rep1_S114"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:51:07.165063+00:00",
"file_format": "fastq",
"file_size": 22272483,
"href": "/sequence-files/IGVFFI2576YRDI/@@download/IGVFFI2576YRDI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/8f3c1113-a1db-41bd-b7a5-f56c55a8ce79/IGVFFI2576YRDI.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-FF1-BinF-PCR1-Rep1_S114_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0978YZEF/",
"accession": "IGVFFI0978YZEF",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF1-BinF-PCR1-Rep1_S114"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:42:02.503181+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI0978YZEF/@@download/IGVFFI0978YZEF.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/fb7e525e-adb8-4744-b3cf-3de198e5983b/IGVFFI0978YZEF.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF1-BinF-PCR1-Rep1_S114.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8149ZFKP/",
"accession": "IGVFFI8149ZFKP",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF1-BinF-PCR2-Rep1_S120"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:51:25.640751+00:00",
"file_format": "fastq",
"file_size": 24747787,
"href": "/sequence-files/IGVFFI8149ZFKP/@@download/IGVFFI8149ZFKP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/bda80f1e-61c9-48c1-a4e7-66e9352bae5b/IGVFFI8149ZFKP.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-FF1-BinF-PCR2-Rep1_S120_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4783GBNK/",
"accession": "IGVFFI4783GBNK",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF1-BinF-PCR3-Rep1_S168"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:51:44.617302+00:00",
"file_format": "fastq",
"file_size": 32360808,
"href": "/sequence-files/IGVFFI4783GBNK/@@download/IGVFFI4783GBNK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/7b035173-ed36-4ade-b66d-ae68ac6b6809/IGVFFI4783GBNK.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-FF1-BinF-PCR3-Rep1_S168_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5568QDEG/",
"accession": "IGVFFI5568QDEG",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF1-BinF-PCR4-Rep1_S174"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:52:03.866451+00:00",
"file_format": "fastq",
"file_size": 35909910,
"href": "/sequence-files/IGVFFI5568QDEG/@@download/IGVFFI5568QDEG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/dca53366-dbca-4db0-ac2e-7cec9b4638a9/IGVFFI5568QDEG.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-FF1-BinF-PCR4-Rep1_S174_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3382VPDH/",
"accession": "IGVFFI3382VPDH",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF1-BinF-PCR3-Rep1_S168"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:42:30.866460+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI3382VPDH/@@download/IGVFFI3382VPDH.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/d0731797-1c2c-42d3-befd-781eb9537c4e/IGVFFI3382VPDH.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF1-BinF-PCR3-Rep1_S168.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6386TNSY/",
"accession": "IGVFFI6386TNSY",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF1-BinF-PCR2-Rep1_S120"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:42:17.732548+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI6386TNSY/@@download/IGVFFI6386TNSY.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/073fe174-23a9-4ed8-94c6-a5374dfb67fe/IGVFFI6386TNSY.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF1-BinF-PCR2-Rep1_S120.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0298DADK/",
"accession": "IGVFFI0298DADK",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF1-BinF-PCR4-Rep1_S174"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:42:44.189975+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI0298DADK/@@download/IGVFFI0298DADK.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/573e5b92-ba48-4dd9-a4f6-84b03d062009/IGVFFI0298DADK.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF1-BinF-PCR4-Rep1_S174.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS2269HBNS/",
"accession": "IGVFDS2269HBNS",
"aliases": [
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF1-BinF-PCR1-Rep1_S114",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF1-BinF-PCR2-Rep1_S120",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF1-BinF-PCR3-Rep1_S168",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF1-BinF-PCR4-Rep1_S174"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:11:15.453876+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM6177XAAS/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6177XAAS",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF1-BinF-PCR1-Rep1_S114",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF1-BinF-PCR2-Rep1_S120",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF1-BinF-PCR3-Rep1_S168",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF1-BinF-PCR4-Rep1_S174"
],
"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 F for 80-100% 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": "2024-06-01T01:51:07.165063+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "a599a8a7-4e3c-4ba5-8f59-f6779fe0790b"
}