{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS9328UUVN/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS9328UUVN",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF2-BinF-PCR1-Rep1_S150",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF2-BinF-PCR2-Rep1_S156",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF2-BinF-PCR3-Rep1_S204",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF2-BinF-PCR4-Rep1_S210"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM2356KPRX](/in-vitro-systems/IGVFSM2356KPRX/) 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/IGVFSM2356KPRX/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM2356KPRX](/in-vitro-systems/IGVFSM2356KPRX/) 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/IGVFSM2356KPRX/"
},
{
"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 [IGVFDS9328UUVN](/auxiliary-sets/IGVFDS9328UUVN/) has sequence file(s) [IGVFFI8430IXFV](/sequence-files/IGVFFI8430IXFV/), [IGVFFI8166TMOU](/sequence-files/IGVFFI8166TMOU/), [IGVFFI8480BRGG](/sequence-files/IGVFFI8480BRGG/), [IGVFFI8181DYGV](/sequence-files/IGVFFI8181DYGV/) 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/IGVFDS9328UUVN/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS9328UUVN](/auxiliary-sets/IGVFDS9328UUVN/) 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/IGVFDS9328UUVN/"
}
]
},
"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": "2024-05-14T16:51:37.311709+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/IGVFFI8430IXFV/",
"accession": "IGVFFI8430IXFV",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF2-BinF-PCR1-Rep1_S150"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:54:48.144894+00:00",
"file_format": "fastq",
"file_size": 18316143,
"href": "/sequence-files/IGVFFI8430IXFV/@@download/IGVFFI8430IXFV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/9b68bd2a-7f05-4533-a071-3bf5fb2eb277/IGVFFI8430IXFV.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-BinF-PCR1-Rep1_S150_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9000DITZ/",
"accession": "IGVFFI9000DITZ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF2-BinF-PCR1-Rep1_S150"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:44:49.239577+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI9000DITZ/@@download/IGVFFI9000DITZ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/fb6a6dbe-0b76-4c8f-92be-a3c2edc2473e/IGVFFI9000DITZ.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF2-BinF-PCR1-Rep1_S150.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8166TMOU/",
"accession": "IGVFFI8166TMOU",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF2-BinF-PCR3-Rep1_S204"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:55:24.930504+00:00",
"file_format": "fastq",
"file_size": 26219982,
"href": "/sequence-files/IGVFFI8166TMOU/@@download/IGVFFI8166TMOU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/95d24e65-7d4b-4d9e-9668-a2d72c401e9f/IGVFFI8166TMOU.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-BinF-PCR3-Rep1_S204_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8480BRGG/",
"accession": "IGVFFI8480BRGG",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF2-BinF-PCR2-Rep1_S156"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:55:06.412526+00:00",
"file_format": "fastq",
"file_size": 16085143,
"href": "/sequence-files/IGVFFI8480BRGG/@@download/IGVFFI8480BRGG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/3e117dc8-971b-4ddc-97bd-1ee7cdc7286e/IGVFFI8480BRGG.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-BinF-PCR2-Rep1_S156_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8181DYGV/",
"accession": "IGVFFI8181DYGV",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF2-BinF-PCR4-Rep1_S210"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:55:42.856384+00:00",
"file_format": "fastq",
"file_size": 27609239,
"href": "/sequence-files/IGVFFI8181DYGV/@@download/IGVFFI8181DYGV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/a4f31601-64b2-4549-8313-0ce6b6dbe4fc/IGVFFI8181DYGV.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-BinF-PCR4-Rep1_S210_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7169ITED/",
"accession": "IGVFFI7169ITED",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF2-BinF-PCR2-Rep1_S156"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:45:02.917201+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI7169ITED/@@download/IGVFFI7169ITED.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/460cf5f8-1f19-467d-ba50-b94583531ab9/IGVFFI7169ITED.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF2-BinF-PCR2-Rep1_S156.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0106NXXW/",
"accession": "IGVFFI0106NXXW",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF2-BinF-PCR3-Rep1_S204"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:45:16.410462+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI0106NXXW/@@download/IGVFFI0106NXXW.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/43a4486b-126b-4e51-92f0-53c7dfc11e07/IGVFFI0106NXXW.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF2-BinF-PCR3-Rep1_S204.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4656ZGKK/",
"accession": "IGVFFI4656ZGKK",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF2-BinF-PCR4-Rep1_S210"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:45:30.021186+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI4656ZGKK/@@download/IGVFFI4656ZGKK.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/6f1581a4-eead-4e95-ad5c-a0bd6e7c7d7f/IGVFFI4656ZGKK.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF2-BinF-PCR4-Rep1_S210.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS9034AAFA/",
"accession": "IGVFDS9034AAFA",
"aliases": [
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF2-BinF-PCR1-Rep1_S150",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF2-BinF-PCR2-Rep1_S156",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF2-BinF-PCR3-Rep1_S204",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF2-BinF-PCR4-Rep1_S210"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:13:24.477610+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2356KPRX/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2356KPRX",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF2-BinF-PCR1-Rep1_S150",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF2-BinF-PCR2-Rep1_S156",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF2-BinF-PCR3-Rep1_S204",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF2-BinF-PCR4-Rep1_S210"
],
"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 F for 80-100% 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": "2024-06-01T01:54:48.144894+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "c6f34502-a2a9-44e9-a6d5-47fbb1a4a3f3"
}