{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS2912NRFL/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS2912NRFL",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinA-PCR1_S1",
"jesse-engreitz:auxiliary_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinA-PCR2_S97",
"jesse-engreitz:auxiliary_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinA-PCR3_S193",
"jesse-engreitz:auxiliary_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinA-PCR4_S289"
],
"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 [IGVFSM0561OELB](/in-vitro-systems/IGVFSM0561OELB/) 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/IGVFSM0561OELB/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM0561OELB](/in-vitro-systems/IGVFSM0561OELB/) 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/IGVFSM0561OELB/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS2912NRFL](/auxiliary-sets/IGVFDS2912NRFL/) has sequence file(s) [IGVFFI6104EBTD](/sequence-files/IGVFFI6104EBTD/), [IGVFFI0114BAKO](/sequence-files/IGVFFI0114BAKO/), [IGVFFI5675LJMW](/sequence-files/IGVFFI5675LJMW/), [IGVFFI0686TXEM](/sequence-files/IGVFFI0686TXEM/) 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/IGVFDS2912NRFL/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS2912NRFL](/auxiliary-sets/IGVFDS2912NRFL/) 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/IGVFDS2912NRFL/"
}
]
},
"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": "2024-05-06T23:13:25.170837+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/IGVFFI6104EBTD/",
"accession": "IGVFFI6104EBTD",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinA-PCR1_S1"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:24:29.141534+00:00",
"file_format": "fastq",
"file_size": 3282173,
"href": "/sequence-files/IGVFFI6104EBTD/@@download/IGVFFI6104EBTD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/f854521a-fe29-4da8-af7d-62f2d66398f8/IGVFFI6104EBTD.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/210301B002-CohesinFF/fastq/CCND1-Auxin6hrs-FF1-BinA-PCR1_S1_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5232UHXW/",
"accession": "IGVFFI5232UHXW",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinA-PCR1_S1"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:22:29.967140+00:00",
"file_format": "yaml",
"file_size": 906,
"href": "/configuration-files/IGVFFI5232UHXW/@@download/IGVFFI5232UHXW.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/c13c37bc-ae6e-47a3-a68a-03fb00e51287/IGVFFI5232UHXW.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin6hrs-FF1-BinA-PCR1_S1.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0114BAKO/",
"accession": "IGVFFI0114BAKO",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinA-PCR2_S97"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:24:55.307128+00:00",
"file_format": "fastq",
"file_size": 5844731,
"href": "/sequence-files/IGVFFI0114BAKO/@@download/IGVFFI0114BAKO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/bab634b5-8f78-46ca-8ffb-0b072d69b828/IGVFFI0114BAKO.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/210301B002-CohesinFF/fastq/CCND1-Auxin6hrs-FF1-BinA-PCR2_S97_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5675LJMW/",
"accession": "IGVFFI5675LJMW",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinA-PCR3_S193"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:25:11.390950+00:00",
"file_format": "fastq",
"file_size": 4625347,
"href": "/sequence-files/IGVFFI5675LJMW/@@download/IGVFFI5675LJMW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/e3f5ce44-be16-4f5c-9d47-3dfc082c0034/IGVFFI5675LJMW.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/210301B002-CohesinFF/fastq/CCND1-Auxin6hrs-FF1-BinA-PCR3_S193_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9105HSUU/",
"accession": "IGVFFI9105HSUU",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinA-PCR3_S193"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:23:21.236184+00:00",
"file_format": "yaml",
"file_size": 910,
"href": "/configuration-files/IGVFFI9105HSUU/@@download/IGVFFI9105HSUU.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/21dd60a8-b5c3-4f9d-ba76-8356c02838c4/IGVFFI9105HSUU.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin6hrs-FF1-BinA-PCR3_S193.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0686TXEM/",
"accession": "IGVFFI0686TXEM",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinA-PCR4_S289"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:25:27.376029+00:00",
"file_format": "fastq",
"file_size": 3946742,
"href": "/sequence-files/IGVFFI0686TXEM/@@download/IGVFFI0686TXEM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/0a2937ab-c49f-434f-a669-88001cc5059b/IGVFFI0686TXEM.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/210301B002-CohesinFF/fastq/CCND1-Auxin6hrs-FF1-BinA-PCR4_S289_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9317QGFN/",
"accession": "IGVFFI9317QGFN",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinA-PCR4_S289"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:23:34.930097+00:00",
"file_format": "yaml",
"file_size": 909,
"href": "/configuration-files/IGVFFI9317QGFN/@@download/IGVFFI9317QGFN.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/5557d0e1-f7ae-4093-8c8a-15b1c6acd6a2/IGVFFI9317QGFN.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin6hrs-FF1-BinA-PCR4_S289.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6952QEIT/",
"accession": "IGVFFI6952QEIT",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinA-PCR2_S97"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:23:07.479109+00:00",
"file_format": "yaml",
"file_size": 907,
"href": "/configuration-files/IGVFFI6952QEIT/@@download/IGVFFI6952QEIT.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/8d19f6db-7b08-44be-b48e-03c4d88bb012/IGVFFI6952QEIT.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin6hrs-FF1-BinA-PCR2_S97.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS0964GIQS/",
"accession": "IGVFDS0964GIQS",
"aliases": [
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinA-PCR1_S1",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinA-PCR2_S97",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinA-PCR3_S193",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinA-PCR4_S289"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:22:59.355853+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0561OELB/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0561OELB",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinA-PCR1_S1",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinA-PCR2_S97",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinA-PCR3_S193",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinA-PCR4_S289"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS0392OWNZ/"
],
"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 A for 0-10% expression of CCND1) 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": "2024-06-01T01:24:29.141534+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in 36 genomic loci",
"uuid": "1de65850-0bfb-4522-aec0-18dacfa88aa9"
}