{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS5389PFCH/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS5389PFCH",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinC-PCR1_S3",
"jesse-engreitz:auxiliary_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinC-PCR2_S99",
"jesse-engreitz:auxiliary_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinC-PCR3_S195",
"jesse-engreitz:auxiliary_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinC-PCR4_S291"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM6480FETB](/in-vitro-systems/IGVFSM6480FETB/) 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/IGVFSM6480FETB/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM6480FETB](/in-vitro-systems/IGVFSM6480FETB/) 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/IGVFSM6480FETB/"
},
{
"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 [IGVFDS5389PFCH](/auxiliary-sets/IGVFDS5389PFCH/) has sequence file(s) [IGVFFI2761AOAR](/sequence-files/IGVFFI2761AOAR/), [IGVFFI6827FMYI](/sequence-files/IGVFFI6827FMYI/), [IGVFFI2191UDNG](/sequence-files/IGVFFI2191UDNG/), [IGVFFI5612HJRS](/sequence-files/IGVFFI5612HJRS/) 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/IGVFDS5389PFCH/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS5389PFCH](/auxiliary-sets/IGVFDS5389PFCH/) 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/IGVFDS5389PFCH/"
}
]
},
"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": "2024-05-06T23:13:28.115930+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/IGVFFI2761AOAR/",
"accession": "IGVFFI2761AOAR",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinC-PCR1_S3"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:24:43.745452+00:00",
"file_format": "fastq",
"file_size": 5675294,
"href": "/sequence-files/IGVFFI2761AOAR/@@download/IGVFFI2761AOAR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/f81224e2-392f-4f4d-8c12-36a03a779cfd/IGVFFI2761AOAR.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/210301B002-CohesinFF/fastq/CCND1-Auxin6hrs-FF1-BinC-PCR1_S3_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0324BUPW/",
"accession": "IGVFFI0324BUPW",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinC-PCR1_S3"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:22:57.717231+00:00",
"file_format": "yaml",
"file_size": 905,
"href": "/configuration-files/IGVFFI0324BUPW/@@download/IGVFFI0324BUPW.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/67c51a73-3d25-4928-8b9b-6dd17ef45258/IGVFFI0324BUPW.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin6hrs-FF1-BinC-PCR1_S3.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6827FMYI/",
"accession": "IGVFFI6827FMYI",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinC-PCR4_S291"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:25:32.354053+00:00",
"file_format": "fastq",
"file_size": 6899881,
"href": "/sequence-files/IGVFFI6827FMYI/@@download/IGVFFI6827FMYI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/b83ad32c-03aa-44b1-8361-9050ff2bb04a/IGVFFI6827FMYI.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/210301B002-CohesinFF/fastq/CCND1-Auxin6hrs-FF1-BinC-PCR4_S291_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2191UDNG/",
"accession": "IGVFFI2191UDNG",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinC-PCR2_S99"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:25:00.480408+00:00",
"file_format": "fastq",
"file_size": 7816883,
"href": "/sequence-files/IGVFFI2191UDNG/@@download/IGVFFI2191UDNG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/6e1958c6-580f-4ff0-9fca-849d53cce21d/IGVFFI2191UDNG.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/210301B002-CohesinFF/fastq/CCND1-Auxin6hrs-FF1-BinC-PCR2_S99_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5612HJRS/",
"accession": "IGVFFI5612HJRS",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinC-PCR3_S195"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:25:16.926009+00:00",
"file_format": "fastq",
"file_size": 7863756,
"href": "/sequence-files/IGVFFI5612HJRS/@@download/IGVFFI5612HJRS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/15c4c816-244b-48bc-8a25-c118caa67699/IGVFFI5612HJRS.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/210301B002-CohesinFF/fastq/CCND1-Auxin6hrs-FF1-BinC-PCR3_S195_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2434JICM/",
"accession": "IGVFFI2434JICM",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinC-PCR2_S99"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:23:11.923535+00:00",
"file_format": "yaml",
"file_size": 907,
"href": "/configuration-files/IGVFFI2434JICM/@@download/IGVFFI2434JICM.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/1f38da5f-824d-4ce1-bcd6-c8a3f696b7fa/IGVFFI2434JICM.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin6hrs-FF1-BinC-PCR2_S99.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9949JLMY/",
"accession": "IGVFFI9949JLMY",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinC-PCR4_S291"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:23:39.402440+00:00",
"file_format": "yaml",
"file_size": 910,
"href": "/configuration-files/IGVFFI9949JLMY/@@download/IGVFFI9949JLMY.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/ad6bc740-2d7a-43d6-8aa9-21d98f68bf64/IGVFFI9949JLMY.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin6hrs-FF1-BinC-PCR4_S291.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0690VWRF/",
"accession": "IGVFFI0690VWRF",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinC-PCR3_S195"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:23:25.880187+00:00",
"file_format": "yaml",
"file_size": 908,
"href": "/configuration-files/IGVFFI0690VWRF/@@download/IGVFFI0690VWRF.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/b3a2a20f-17f6-4cf5-acd7-ec13c9c94a08/IGVFFI0690VWRF.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin6hrs-FF1-BinC-PCR3_S195.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS8571HTVZ/",
"accession": "IGVFDS8571HTVZ",
"aliases": [
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinC-PCR1_S3",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinC-PCR2_S99",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinC-PCR3_S195",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinC-PCR4_S291"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:23:13.199719+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM6480FETB/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6480FETB",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinC-PCR1_S3",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinC-PCR2_S99",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinC-PCR3_S195",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinC-PCR4_S291"
],
"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 C for 35-45% 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": "2024-06-01T01:24:43.745452+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in 36 genomic loci",
"uuid": "d923dd48-86d3-4330-8814-c466d76d0ab6"
}