{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS0887BEDU/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS0887BEDU",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF2-BinC-PCR1-Rep1_S147",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF2-BinC-PCR2-Rep1_S153",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF2-BinC-PCR3-Rep1_S201",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF2-BinC-PCR4-Rep1_S207"
],
"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 [IGVFSM5674HHJF](/in-vitro-systems/IGVFSM5674HHJF/) 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/IGVFSM5674HHJF/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM5674HHJF](/in-vitro-systems/IGVFSM5674HHJF/) 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/IGVFSM5674HHJF/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS0887BEDU](/auxiliary-sets/IGVFDS0887BEDU/) has sequence file(s) [IGVFFI6284GDRW](/sequence-files/IGVFFI6284GDRW/), [IGVFFI6670CCCW](/sequence-files/IGVFFI6670CCCW/), [IGVFFI4732FGXM](/sequence-files/IGVFFI4732FGXM/), [IGVFFI9975SRBC](/sequence-files/IGVFFI9975SRBC/) 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/IGVFDS0887BEDU/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS0887BEDU](/auxiliary-sets/IGVFDS0887BEDU/) 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/IGVFDS0887BEDU/"
}
]
},
"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": "2024-05-14T16:51:34.602209+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/IGVFFI6284GDRW/",
"accession": "IGVFFI6284GDRW",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF2-BinC-PCR1-Rep1_S147"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:54:39.030311+00:00",
"file_format": "fastq",
"file_size": 15588192,
"href": "/sequence-files/IGVFFI6284GDRW/@@download/IGVFFI6284GDRW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/2c1926a6-e693-46e6-809d-e99a3f20e763/IGVFFI6284GDRW.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-BinC-PCR1-Rep1_S147_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9955CJZS/",
"accession": "IGVFFI9955CJZS",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF2-BinC-PCR1-Rep1_S147"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:44:41.481369+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI9955CJZS/@@download/IGVFFI9955CJZS.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/e3c701e3-811d-40f0-b21a-7b417b364a63/IGVFFI9955CJZS.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF2-BinC-PCR1-Rep1_S147.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6670CCCW/",
"accession": "IGVFFI6670CCCW",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF2-BinC-PCR4-Rep1_S207"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:55:34.312744+00:00",
"file_format": "fastq",
"file_size": 6218387,
"href": "/sequence-files/IGVFFI6670CCCW/@@download/IGVFFI6670CCCW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/2dfe7547-9ebc-4f6f-99f3-d6547241aad1/IGVFFI6670CCCW.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-BinC-PCR4-Rep1_S207_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8571MRWS/",
"accession": "IGVFFI8571MRWS",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF2-BinC-PCR4-Rep1_S207"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:45:22.967263+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI8571MRWS/@@download/IGVFFI8571MRWS.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/17a4abdc-c6e7-45b8-a9c8-6a0fe1814ca2/IGVFFI8571MRWS.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF2-BinC-PCR4-Rep1_S207.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4732FGXM/",
"accession": "IGVFFI4732FGXM",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF2-BinC-PCR2-Rep1_S153"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:54:57.393409+00:00",
"file_format": "fastq",
"file_size": 7486318,
"href": "/sequence-files/IGVFFI4732FGXM/@@download/IGVFFI4732FGXM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/1340cce3-01ed-4dfc-a4ad-091685c639f1/IGVFFI4732FGXM.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-BinC-PCR2-Rep1_S153_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9975SRBC/",
"accession": "IGVFFI9975SRBC",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF2-BinC-PCR3-Rep1_S201"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:55:15.554298+00:00",
"file_format": "fastq",
"file_size": 26528834,
"href": "/sequence-files/IGVFFI9975SRBC/@@download/IGVFFI9975SRBC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/8b82bc36-58c8-4314-a10d-0f4885ca9749/IGVFFI9975SRBC.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-BinC-PCR3-Rep1_S201_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4903FZPN/",
"accession": "IGVFFI4903FZPN",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF2-BinC-PCR2-Rep1_S153"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:44:55.973022+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI4903FZPN/@@download/IGVFFI4903FZPN.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/386ea622-5e72-4d3b-b117-a6a0563c50ea/IGVFFI4903FZPN.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF2-BinC-PCR2-Rep1_S153.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0190JMYM/",
"accession": "IGVFFI0190JMYM",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF2-BinC-PCR3-Rep1_S201"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:45:09.635159+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI0190JMYM/@@download/IGVFFI0190JMYM.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/928bf542-6a10-42af-8a03-7a482ef23d79/IGVFFI0190JMYM.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF2-BinC-PCR3-Rep1_S201.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS3361ABEP/",
"accession": "IGVFDS3361ABEP",
"aliases": [
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF2-BinC-PCR1-Rep1_S147",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF2-BinC-PCR2-Rep1_S153",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF2-BinC-PCR3-Rep1_S201",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF2-BinC-PCR4-Rep1_S207"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:13:03.873576+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5674HHJF/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5674HHJF",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF2-BinC-PCR1-Rep1_S147",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF2-BinC-PCR2-Rep1_S153",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF2-BinC-PCR3-Rep1_S201",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF2-BinC-PCR4-Rep1_S207"
],
"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 C for 35-45% 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": "2024-06-01T01:54:39.030311+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "7b6f468d-967a-4649-8f7c-de810c1c4636"
}