{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS3352ZNFQ/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS3352ZNFQ",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinA-PCR1_S73",
"jesse-engreitz:auxiliary_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinA-PCR2_S169",
"jesse-engreitz:auxiliary_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinA-PCR3_S265",
"jesse-engreitz:auxiliary_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinA-PCR4_S361"
],
"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/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS3352ZNFQ](/auxiliary-sets/IGVFDS3352ZNFQ/) has sequence file(s) [IGVFFI3567ECNQ](/sequence-files/IGVFFI3567ECNQ/), [IGVFFI1611MQSG](/sequence-files/IGVFFI1611MQSG/), [IGVFFI1011WVNT](/sequence-files/IGVFFI1011WVNT/), [IGVFFI1597PAXC](/sequence-files/IGVFFI1597PAXC/) 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/IGVFDS3352ZNFQ/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS3352ZNFQ](/auxiliary-sets/IGVFDS3352ZNFQ/) 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/IGVFDS3352ZNFQ/"
}
]
},
"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": "2024-05-06T23:13:48.280745+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/IGVFFI3567ECNQ/",
"accession": "IGVFFI3567ECNQ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinA-PCR1_S73"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:29:12.448220+00:00",
"file_format": "fastq",
"file_size": 3768611,
"href": "/sequence-files/IGVFFI3567ECNQ/@@download/IGVFFI3567ECNQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/24cd9a75-f0e0-450d-a39b-f5550616214c/IGVFFI3567ECNQ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/210301B002-CohesinFF/fastq/CCND1-Auxin0hrs-FF1-BinA-PCR1_S73_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4517BOFT/",
"accession": "IGVFFI4517BOFT",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinA-PCR1_S73"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:23:48.446439+00:00",
"file_format": "yaml",
"file_size": 907,
"href": "/configuration-files/IGVFFI4517BOFT/@@download/IGVFFI4517BOFT.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/5e5de2f3-5174-47ef-a522-67147b924ad6/IGVFFI4517BOFT.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin0hrs-FF1-BinA-PCR1_S73.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4133KBSX/",
"accession": "IGVFFI4133KBSX",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinA-PCR2_S169"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:24:01.442311+00:00",
"file_format": "yaml",
"file_size": 909,
"href": "/configuration-files/IGVFFI4133KBSX/@@download/IGVFFI4133KBSX.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/07649c01-c324-4d8d-b87e-f1cd3e7a54a5/IGVFFI4133KBSX.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin0hrs-FF1-BinA-PCR2_S169.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1611MQSG/",
"accession": "IGVFFI1611MQSG",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinA-PCR2_S169"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:29:28.134153+00:00",
"file_format": "fastq",
"file_size": 7306295,
"href": "/sequence-files/IGVFFI1611MQSG/@@download/IGVFFI1611MQSG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/6e48eefb-f6c8-4ea4-988f-f4a6275b7b68/IGVFFI1611MQSG.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/210301B002-CohesinFF/fastq/CCND1-Auxin0hrs-FF1-BinA-PCR2_S169_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1011WVNT/",
"accession": "IGVFFI1011WVNT",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinA-PCR3_S265"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:29:43.806818+00:00",
"file_format": "fastq",
"file_size": 6368053,
"href": "/sequence-files/IGVFFI1011WVNT/@@download/IGVFFI1011WVNT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/81c7a41d-1da3-4cfd-b17e-4fcef475e62a/IGVFFI1011WVNT.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/210301B002-CohesinFF/fastq/CCND1-Auxin0hrs-FF1-BinA-PCR3_S265_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1597PAXC/",
"accession": "IGVFFI1597PAXC",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinA-PCR4_S361"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:30:00.738447+00:00",
"file_format": "fastq",
"file_size": 7325011,
"href": "/sequence-files/IGVFFI1597PAXC/@@download/IGVFFI1597PAXC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/777a051b-b55f-4f2e-a8f2-71e179eb1d5e/IGVFFI1597PAXC.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/210301B002-CohesinFF/fastq/CCND1-Auxin0hrs-FF1-BinA-PCR4_S361_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1582BSGK/",
"accession": "IGVFFI1582BSGK",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinA-PCR4_S361"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:24:28.078052+00:00",
"file_format": "yaml",
"file_size": 908,
"href": "/configuration-files/IGVFFI1582BSGK/@@download/IGVFFI1582BSGK.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/397e6f90-9c82-4364-b260-ff02a7e57f2a/IGVFFI1582BSGK.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin0hrs-FF1-BinA-PCR4_S361.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0209ENJY/",
"accession": "IGVFFI0209ENJY",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinA-PCR3_S265"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:24:14.747347+00:00",
"file_format": "yaml",
"file_size": 908,
"href": "/configuration-files/IGVFFI0209ENJY/@@download/IGVFFI0209ENJY.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/638ec703-0ae4-460f-8a1b-f1d586da8af4/IGVFFI0209ENJY.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin0hrs-FF1-BinA-PCR3_S265.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS8123YLWP/",
"accession": "IGVFDS8123YLWP",
"aliases": [
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinA-PCR1_S73",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinA-PCR2_S169",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinA-PCR3_S265",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinA-PCR4_S361"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:22:18.762781+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7865RIGH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7865RIGH",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinA-PCR1_S73",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinA-PCR2_S169",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinA-PCR3_S265",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinA-PCR4_S361"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS0392OWNZ/"
],
"modifications": [
"/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) modified with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "11",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-01T01:29:12.448220+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in 36 genomic loci",
"uuid": "840d6513-8da0-4737-b571-8aee13c67f04"
}