{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS2217TMIN/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS2217TMIN",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF2-BinE-PCR1-Rep1_S149",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF2-BinE-PCR2-Rep1_S155",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF2-BinE-PCR3-Rep1_S203",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF2-BinE-PCR4-Rep1_S209"
],
"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/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM2128WJNF](/in-vitro-systems/IGVFSM2128WJNF/) has in progress subobject degron modification [95081d1b-08b4-49ed-b324-e53fc43d8456](/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM2128WJNF/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM2128WJNF](/in-vitro-systems/IGVFSM2128WJNF/) has in progress subobject treatment [d35868d1-c45b-49ae-8ff3-a9c0c22551c2](/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM2128WJNF/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS2217TMIN](/auxiliary-sets/IGVFDS2217TMIN/) has sequence file(s) [IGVFFI4526LHYV](/sequence-files/IGVFFI4526LHYV/), [IGVFFI0163GSPS](/sequence-files/IGVFFI0163GSPS/), [IGVFFI1131GMAD](/sequence-files/IGVFFI1131GMAD/), [IGVFFI6998PWBA](/sequence-files/IGVFFI6998PWBA/) 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/IGVFDS2217TMIN/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS2217TMIN](/auxiliary-sets/IGVFDS2217TMIN/) 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/IGVFDS2217TMIN/"
}
]
},
"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": "2024-05-14T16:51:36.411842+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/IGVFFI4526LHYV/",
"accession": "IGVFFI4526LHYV",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF2-BinE-PCR1-Rep1_S149"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:54:45.148582+00:00",
"file_format": "fastq",
"file_size": 23122507,
"href": "/sequence-files/IGVFFI4526LHYV/@@download/IGVFFI4526LHYV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/d49b8f46-7783-40bb-aea6-c6c014752871/IGVFFI4526LHYV.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/FAM3C-Auxin6hrs-FF2-BinE-PCR1-Rep1_S149_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2005HEDU/",
"accession": "IGVFFI2005HEDU",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF2-BinE-PCR1-Rep1_S149"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:44:47.023281+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI2005HEDU/@@download/IGVFFI2005HEDU.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/126077d6-531d-4967-9864-435ce44afefc/IGVFFI2005HEDU.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF2-BinE-PCR1-Rep1_S149.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0163GSPS/",
"accession": "IGVFFI0163GSPS",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF2-BinE-PCR3-Rep1_S203"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:55:21.746354+00:00",
"file_format": "fastq",
"file_size": 24852380,
"href": "/sequence-files/IGVFFI0163GSPS/@@download/IGVFFI0163GSPS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/21422fd4-58fa-419d-9b1c-e7c9a4c211d5/IGVFFI0163GSPS.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/FAM3C-Auxin6hrs-FF2-BinE-PCR3-Rep1_S203_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1131GMAD/",
"accession": "IGVFFI1131GMAD",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF2-BinE-PCR2-Rep1_S155"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:55:02.967537+00:00",
"file_format": "fastq",
"file_size": 18493746,
"href": "/sequence-files/IGVFFI1131GMAD/@@download/IGVFFI1131GMAD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/f6372321-e727-4634-82dd-692c7f653339/IGVFFI1131GMAD.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/FAM3C-Auxin6hrs-FF2-BinE-PCR2-Rep1_S155_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6998PWBA/",
"accession": "IGVFFI6998PWBA",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF2-BinE-PCR4-Rep1_S209"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:55:39.769285+00:00",
"file_format": "fastq",
"file_size": 25139069,
"href": "/sequence-files/IGVFFI6998PWBA/@@download/IGVFFI6998PWBA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/ef7c05e4-e7c5-4f5f-ac6d-14b627cf9b1a/IGVFFI6998PWBA.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/FAM3C-Auxin6hrs-FF2-BinE-PCR4-Rep1_S209_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4661OPRY/",
"accession": "IGVFFI4661OPRY",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF2-BinE-PCR4-Rep1_S209"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:45:27.594520+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI4661OPRY/@@download/IGVFFI4661OPRY.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/9ff3d49b-0e82-4c30-8c8e-f6685a6ce42a/IGVFFI4661OPRY.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF2-BinE-PCR4-Rep1_S209.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0980GKKZ/",
"accession": "IGVFFI0980GKKZ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF2-BinE-PCR3-Rep1_S203"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:45:13.956115+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI0980GKKZ/@@download/IGVFFI0980GKKZ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/9eace128-d7e7-4650-879b-a76838b3d7f3/IGVFFI0980GKKZ.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF2-BinE-PCR3-Rep1_S203.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8059EUPB/",
"accession": "IGVFFI8059EUPB",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF2-BinE-PCR2-Rep1_S155"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:45:00.492994+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI8059EUPB/@@download/IGVFFI8059EUPB.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/10556c40-dd4f-4df2-ad18-4a51b4a851a9/IGVFFI8059EUPB.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF2-BinE-PCR2-Rep1_S155.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS3498HWDW/",
"accession": "IGVFDS3498HWDW",
"aliases": [
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF2-BinE-PCR1-Rep1_S149",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF2-BinE-PCR2-Rep1_S155",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF2-BinE-PCR3-Rep1_S203",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF2-BinE-PCR4-Rep1_S209"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:13:18.199912+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2128WJNF/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2128WJNF",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF2-BinE-PCR1-Rep1_S149",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF2-BinE-PCR2-Rep1_S155",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF2-BinE-PCR3-Rep1_S203",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF2-BinE-PCR4-Rep1_S209"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS1891GTLU/"
],
"modifications": [
"/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/",
"/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 FAM3C) treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours, modified with a guide library",
"taxa": "Homo sapiens",
"treatments": [
"/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/"
]
}
],
"schema_version": "11",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-01T01:54:45.148582+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "19cda58b-9754-42c0-bcff-d72a966fe4f8"
}