{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS7308SSJS/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS7308SSJS",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF1-BinC-PCR1-Rep1_S135",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF1-BinC-PCR2-Rep1_S141",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF1-BinC-PCR3-Rep1_S189",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF1-BinC-PCR4-Rep1_S195"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM5752WTYA](/in-vitro-systems/IGVFSM5752WTYA/) 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/IGVFSM5752WTYA/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM5752WTYA](/in-vitro-systems/IGVFSM5752WTYA/) 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/IGVFSM5752WTYA/"
},
{
"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 [IGVFDS7308SSJS](/auxiliary-sets/IGVFDS7308SSJS/) has sequence file(s) [IGVFFI6247BYIS](/sequence-files/IGVFFI6247BYIS/), [IGVFFI3369KHSA](/sequence-files/IGVFFI3369KHSA/), [IGVFFI1726SABC](/sequence-files/IGVFFI1726SABC/), [IGVFFI6913STDU](/sequence-files/IGVFFI6913STDU/) 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/IGVFDS7308SSJS/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS7308SSJS](/auxiliary-sets/IGVFDS7308SSJS/) 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/IGVFDS7308SSJS/"
}
]
},
"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": "2024-05-14T16:51:09.241024+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/IGVFFI6247BYIS/",
"accession": "IGVFFI6247BYIS",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF1-BinC-PCR1-Rep1_S135"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:53:25.766652+00:00",
"file_format": "fastq",
"file_size": 29711268,
"href": "/sequence-files/IGVFFI6247BYIS/@@download/IGVFFI6247BYIS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/2a0b544b-46ea-46ce-89ba-5b98e428a7ff/IGVFFI6247BYIS.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-BinC-PCR1-Rep1_S135_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5075XAJF/",
"accession": "IGVFFI5075XAJF",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF1-BinC-PCR1-Rep1_S135"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:43:46.260593+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI5075XAJF/@@download/IGVFFI5075XAJF.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/7e871baa-8987-4315-a75c-bdeeab9bba1c/IGVFFI5075XAJF.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF1-BinC-PCR1-Rep1_S135.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3369KHSA/",
"accession": "IGVFFI3369KHSA",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF1-BinC-PCR3-Rep1_S189"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:54:02.268396+00:00",
"file_format": "fastq",
"file_size": 36565907,
"href": "/sequence-files/IGVFFI3369KHSA/@@download/IGVFFI3369KHSA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/dc931aad-094d-4b6b-9664-7e90d96cd996/IGVFFI3369KHSA.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-BinC-PCR3-Rep1_S189_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1726SABC/",
"accession": "IGVFFI1726SABC",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF1-BinC-PCR2-Rep1_S141"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:53:43.806938+00:00",
"file_format": "fastq",
"file_size": 28363430,
"href": "/sequence-files/IGVFFI1726SABC/@@download/IGVFFI1726SABC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/90d7aa70-ede7-4c04-95ea-155ba6679eb4/IGVFFI1726SABC.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-BinC-PCR2-Rep1_S141_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6913STDU/",
"accession": "IGVFFI6913STDU",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF1-BinC-PCR4-Rep1_S195"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:54:21.051992+00:00",
"file_format": "fastq",
"file_size": 34740332,
"href": "/sequence-files/IGVFFI6913STDU/@@download/IGVFFI6913STDU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/53daa44c-9477-49d4-845f-c37accb68d82/IGVFFI6913STDU.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-BinC-PCR4-Rep1_S195_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7035ZSAZ/",
"accession": "IGVFFI7035ZSAZ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF1-BinC-PCR2-Rep1_S141"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:44:00.243453+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI7035ZSAZ/@@download/IGVFFI7035ZSAZ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/132b2353-fab5-4dca-8175-8ada3bc8c289/IGVFFI7035ZSAZ.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF1-BinC-PCR2-Rep1_S141.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9615WQQN/",
"accession": "IGVFFI9615WQQN",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF1-BinC-PCR3-Rep1_S189"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:44:13.901272+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI9615WQQN/@@download/IGVFFI9615WQQN.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/e725308b-5862-4d61-beac-6b248fed4487/IGVFFI9615WQQN.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF1-BinC-PCR3-Rep1_S189.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9344XDPG/",
"accession": "IGVFFI9344XDPG",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF1-BinC-PCR4-Rep1_S195"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:44:27.724170+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI9344XDPG/@@download/IGVFFI9344XDPG.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/6d6bc907-f34d-4c7e-84e2-1d42a519032a/IGVFFI9344XDPG.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF1-BinC-PCR4-Rep1_S195.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS6992SRVM/",
"accession": "IGVFDS6992SRVM",
"aliases": [
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF1-BinC-PCR1-Rep1_S135",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF1-BinC-PCR2-Rep1_S141",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF1-BinC-PCR3-Rep1_S189",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF1-BinC-PCR4-Rep1_S195"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:12:18.893684+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5752WTYA/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5752WTYA",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF1-BinC-PCR1-Rep1_S135",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF1-BinC-PCR2-Rep1_S141",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF1-BinC-PCR3-Rep1_S189",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF1-BinC-PCR4-Rep1_S195"
],
"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": "2024-06-01T01:53:25.766652+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "9d8a202f-fdda-4049-b271-f68fe6b19689"
}