{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS9525OEUV/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS9525OEUV",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR1-Rep1_S136",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR2-Rep1_S142",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR3-Rep1_S190",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR4-Rep1_S196"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM6928JPHO](/in-vitro-systems/IGVFSM6928JPHO/) 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/IGVFSM6928JPHO/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM6928JPHO](/in-vitro-systems/IGVFSM6928JPHO/) 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/IGVFSM6928JPHO/"
},
{
"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 [IGVFDS9525OEUV](/auxiliary-sets/IGVFDS9525OEUV/) has sequence file(s) [IGVFFI8644ELSX](/sequence-files/IGVFFI8644ELSX/), [IGVFFI5753MODI](/sequence-files/IGVFFI5753MODI/), [IGVFFI8303KMQH](/sequence-files/IGVFFI8303KMQH/), [IGVFFI0003GKTA](/sequence-files/IGVFFI0003GKTA/) 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/IGVFDS9525OEUV/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS9525OEUV](/auxiliary-sets/IGVFDS9525OEUV/) 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/IGVFDS9525OEUV/"
}
]
},
"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": "2024-05-14T16:51:10.193383+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/IGVFFI8644ELSX/",
"accession": "IGVFFI8644ELSX",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR1-Rep1_S136"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:53:28.759279+00:00",
"file_format": "fastq",
"file_size": 23487754,
"href": "/sequence-files/IGVFFI8644ELSX/@@download/IGVFFI8644ELSX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/13ee86c5-a85b-4fc0-be0b-9775e621b630/IGVFFI8644ELSX.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-FF1-BinD-PCR1-Rep1_S136_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2872OELQ/",
"accession": "IGVFFI2872OELQ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR1-Rep1_S136"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:43:48.524116+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI2872OELQ/@@download/IGVFFI2872OELQ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/2a932c52-0b85-415b-a7e1-0023b54fcf03/IGVFFI2872OELQ.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF1-BinD-PCR1-Rep1_S136.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5753MODI/",
"accession": "IGVFFI5753MODI",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR2-Rep1_S142"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:53:47.027427+00:00",
"file_format": "fastq",
"file_size": 16779582,
"href": "/sequence-files/IGVFFI5753MODI/@@download/IGVFFI5753MODI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/a4b41623-608e-4802-b8ef-44b046dd49cb/IGVFFI5753MODI.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-FF1-BinD-PCR2-Rep1_S142_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8303KMQH/",
"accession": "IGVFFI8303KMQH",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR3-Rep1_S190"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:54:05.364093+00:00",
"file_format": "fastq",
"file_size": 31644031,
"href": "/sequence-files/IGVFFI8303KMQH/@@download/IGVFFI8303KMQH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/aeebe66c-e6a6-493d-bb62-4c4b8cc7af8f/IGVFFI8303KMQH.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-FF1-BinD-PCR3-Rep1_S190_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0003GKTA/",
"accession": "IGVFFI0003GKTA",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR4-Rep1_S196"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:54:24.045661+00:00",
"file_format": "fastq",
"file_size": 27878556,
"href": "/sequence-files/IGVFFI0003GKTA/@@download/IGVFFI0003GKTA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/3ced79d6-a73c-471f-a681-db8b71db0241/IGVFFI0003GKTA.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-FF1-BinD-PCR4-Rep1_S196_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0910MBLA/",
"accession": "IGVFFI0910MBLA",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR4-Rep1_S196"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:44:29.977867+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI0910MBLA/@@download/IGVFFI0910MBLA.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/15103a88-96d8-494c-a62b-4372c55c5801/IGVFFI0910MBLA.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF1-BinD-PCR4-Rep1_S196.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9546POQT/",
"accession": "IGVFFI9546POQT",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR2-Rep1_S142"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:44:02.557487+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI9546POQT/@@download/IGVFFI9546POQT.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/b699eadb-d44c-42db-a9c7-a696db179ec6/IGVFFI9546POQT.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF1-BinD-PCR2-Rep1_S142.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6470EGGF/",
"accession": "IGVFFI6470EGGF",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR3-Rep1_S190"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:44:16.301247+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI6470EGGF/@@download/IGVFFI6470EGGF.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/4bf8edef-bc26-4857-ad1f-6a0a5732f3ff/IGVFFI6470EGGF.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF1-BinD-PCR3-Rep1_S190.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS2315UDUR/",
"accession": "IGVFDS2315UDUR",
"aliases": [
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR1-Rep1_S136",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR2-Rep1_S142",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR3-Rep1_S190",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR4-Rep1_S196"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:12:26.448816+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM6928JPHO/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6928JPHO",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR1-Rep1_S136",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR2-Rep1_S142",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR3-Rep1_S190",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR4-Rep1_S196"
],
"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 D for 55-65% 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": "2024-06-01T01:53:28.759279+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "34e5d3e5-3fa4-40c4-a530-ef50ded623a9"
}