{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS8118JQVG/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS8118JQVG",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF2-BinA-PCR1-Rep1_S229",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF2-BinA-PCR2-Rep1_S235",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF2-BinA-PCR3-Rep1_S271",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF2-BinA-PCR4-Rep1_S277"
],
"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 [IGVFDS8118JQVG](/auxiliary-sets/IGVFDS8118JQVG/) has sequence file(s) [IGVFFI0615RGSV](/sequence-files/IGVFFI0615RGSV/), [IGVFFI6047KOFH](/sequence-files/IGVFFI6047KOFH/), [IGVFFI0519KVUX](/sequence-files/IGVFFI0519KVUX/), [IGVFFI6854ADBG](/sequence-files/IGVFFI6854ADBG/) 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/IGVFDS8118JQVG/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS8118JQVG](/auxiliary-sets/IGVFDS8118JQVG/) 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/IGVFDS8118JQVG/"
}
]
},
"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": "2024-05-13T22:39:12.345647+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/IGVFFI0615RGSV/",
"accession": "IGVFFI0615RGSV",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF2-BinA-PCR1-Rep1_S229"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:37:08.484588+00:00",
"file_format": "fastq",
"file_size": 23320711,
"href": "/sequence-files/IGVFFI0615RGSV/@@download/IGVFFI0615RGSV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/3c3146a5-2adf-453a-9112-997aa8cf2be3/IGVFFI0615RGSV.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin0hrs-FF2-BinA-PCR1-Rep1_S229_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2943EDCY/",
"accession": "IGVFFI2943EDCY",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF2-BinA-PCR1-Rep1_S229"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:28:56.265091+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI2943EDCY/@@download/IGVFFI2943EDCY.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/12dfec6f-d818-49fe-b1a1-6f235847c10b/IGVFFI2943EDCY.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF2-BinA-PCR1-Rep1_S229.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6047KOFH/",
"accession": "IGVFFI6047KOFH",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF2-BinA-PCR2-Rep1_S235"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:37:26.620110+00:00",
"file_format": "fastq",
"file_size": 28097259,
"href": "/sequence-files/IGVFFI6047KOFH/@@download/IGVFFI6047KOFH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/da0bc24a-50c6-445a-951c-7b8302c60616/IGVFFI6047KOFH.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin0hrs-FF2-BinA-PCR2-Rep1_S235_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0519KVUX/",
"accession": "IGVFFI0519KVUX",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF2-BinA-PCR3-Rep1_S271"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:37:44.209297+00:00",
"file_format": "fastq",
"file_size": 35315484,
"href": "/sequence-files/IGVFFI0519KVUX/@@download/IGVFFI0519KVUX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/65a69290-91b0-4509-974a-5d24dfc62071/IGVFFI0519KVUX.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin0hrs-FF2-BinA-PCR3-Rep1_S271_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6854ADBG/",
"accession": "IGVFFI6854ADBG",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF2-BinA-PCR4-Rep1_S277"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:38:02.713004+00:00",
"file_format": "fastq",
"file_size": 26494416,
"href": "/sequence-files/IGVFFI6854ADBG/@@download/IGVFFI6854ADBG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/fc9cceed-c92c-4125-9833-9c29b8e8b088/IGVFFI6854ADBG.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin0hrs-FF2-BinA-PCR4-Rep1_S277_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6721PGIX/",
"accession": "IGVFFI6721PGIX",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF2-BinA-PCR4-Rep1_S277"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:29:38.334216+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI6721PGIX/@@download/IGVFFI6721PGIX.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/f7a7fdff-4de9-4036-80d2-015c1783be1f/IGVFFI6721PGIX.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF2-BinA-PCR4-Rep1_S277.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6793LFMG/",
"accession": "IGVFFI6793LFMG",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF2-BinA-PCR2-Rep1_S235"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:29:10.444552+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI6793LFMG/@@download/IGVFFI6793LFMG.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/5ca9ff01-7f12-4b92-8a1e-8f03f877e120/IGVFFI6793LFMG.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF2-BinA-PCR2-Rep1_S235.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2512DSDU/",
"accession": "IGVFFI2512DSDU",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF2-BinA-PCR3-Rep1_S271"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:29:24.338105+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI2512DSDU/@@download/IGVFFI2512DSDU.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/793688c4-26bd-414d-a4cf-aef65322827c/IGVFFI2512DSDU.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF2-BinA-PCR3-Rep1_S271.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS5549RUFF/",
"accession": "IGVFDS5549RUFF",
"aliases": [
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF2-BinA-PCR1-Rep1_S229",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF2-BinA-PCR2-Rep1_S235",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF2-BinA-PCR3-Rep1_S271",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF2-BinA-PCR4-Rep1_S277"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:08:31.314876+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9327YPCM/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9327YPCM",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF2-BinA-PCR1-Rep1_S229",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF2-BinA-PCR2-Rep1_S235",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF2-BinA-PCR3-Rep1_S271",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF2-BinA-PCR4-Rep1_S277"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS6351FGNG/"
],
"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": "2024-06-01T01:37:08.484588+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "5f5f4b97-a7cf-4c5e-95b9-51d0abaf8624"
}