{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS0803KKZH/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS0803KKZH",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF2-BinF-PCR1-Rep1_S126",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF2-BinF-PCR2-Rep1_S132",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF2-BinF-PCR3-Rep1_S180",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF2-BinF-PCR4-Rep1_S186"
],
"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 [IGVFDS0803KKZH](/auxiliary-sets/IGVFDS0803KKZH/) has sequence file(s) [IGVFFI3507JHKO](/sequence-files/IGVFFI3507JHKO/), [IGVFFI7793HRXV](/sequence-files/IGVFFI7793HRXV/), [IGVFFI7085ICFZ](/sequence-files/IGVFFI7085ICFZ/), [IGVFFI6643LUII](/sequence-files/IGVFFI6643LUII/) 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/IGVFDS0803KKZH/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS0803KKZH](/auxiliary-sets/IGVFDS0803KKZH/) 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/IGVFDS0803KKZH/"
}
]
},
"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": "2024-05-14T16:24:23.981506+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/IGVFFI3507JHKO/",
"accession": "IGVFFI3507JHKO",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF2-BinF-PCR1-Rep1_S126"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:52:22.104712+00:00",
"file_format": "fastq",
"file_size": 28778627,
"href": "/sequence-files/IGVFFI3507JHKO/@@download/IGVFFI3507JHKO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/e6f663bf-0cf0-4839-8c91-944914fbd759/IGVFFI3507JHKO.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/FAM3C-Auxin0hrs-FF2-BinF-PCR1-Rep1_S126_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4303KRTG/",
"accession": "IGVFFI4303KRTG",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF2-BinF-PCR1-Rep1_S126"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:42:57.683626+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI4303KRTG/@@download/IGVFFI4303KRTG.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/7d215708-2e67-4035-9005-c3c1cd87e75b/IGVFFI4303KRTG.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF2-BinF-PCR1-Rep1_S126.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8140XRRA/",
"accession": "IGVFFI8140XRRA",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF2-BinF-PCR2-Rep1_S132"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:43:11.341753+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI8140XRRA/@@download/IGVFFI8140XRRA.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/4013fc4c-6be8-4b7c-9c29-460520200fd8/IGVFFI8140XRRA.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF2-BinF-PCR2-Rep1_S132.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7793HRXV/",
"accession": "IGVFFI7793HRXV",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF2-BinF-PCR2-Rep1_S132"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:52:40.154073+00:00",
"file_format": "fastq",
"file_size": 23971288,
"href": "/sequence-files/IGVFFI7793HRXV/@@download/IGVFFI7793HRXV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/93f01b58-212d-4652-afa9-97427055093b/IGVFFI7793HRXV.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/FAM3C-Auxin0hrs-FF2-BinF-PCR2-Rep1_S132_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7085ICFZ/",
"accession": "IGVFFI7085ICFZ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF2-BinF-PCR3-Rep1_S180"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:52:58.282324+00:00",
"file_format": "fastq",
"file_size": 41969951,
"href": "/sequence-files/IGVFFI7085ICFZ/@@download/IGVFFI7085ICFZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/8014f949-476d-4628-a8e7-178340dcec94/IGVFFI7085ICFZ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/FAM3C-Auxin0hrs-FF2-BinF-PCR3-Rep1_S180_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6643LUII/",
"accession": "IGVFFI6643LUII",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF2-BinF-PCR4-Rep1_S186"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:53:16.566885+00:00",
"file_format": "fastq",
"file_size": 30536690,
"href": "/sequence-files/IGVFFI6643LUII/@@download/IGVFFI6643LUII.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/15dbd0ea-a7d0-4093-8160-efb21ec17d0f/IGVFFI6643LUII.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/FAM3C-Auxin0hrs-FF2-BinF-PCR4-Rep1_S186_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3932WMWI/",
"accession": "IGVFFI3932WMWI",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF2-BinF-PCR4-Rep1_S186"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:43:38.811632+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI3932WMWI/@@download/IGVFFI3932WMWI.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/87a4dced-a321-4a90-8da4-5df3bf1e97df/IGVFFI3932WMWI.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF2-BinF-PCR4-Rep1_S186.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4738IQYH/",
"accession": "IGVFFI4738IQYH",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF2-BinF-PCR3-Rep1_S180"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:43:25.494746+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI4738IQYH/@@download/IGVFFI4738IQYH.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/8571ecc5-225b-4798-881a-2756020ef298/IGVFFI4738IQYH.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF2-BinF-PCR3-Rep1_S180.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS3995SYLS/",
"accession": "IGVFDS3995SYLS",
"aliases": [
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF2-BinF-PCR1-Rep1_S126",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF2-BinF-PCR2-Rep1_S132",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF2-BinF-PCR3-Rep1_S180",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF2-BinF-PCR4-Rep1_S186"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:11:57.189312+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4323ZIMC/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4323ZIMC",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF2-BinF-PCR1-Rep1_S126",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF2-BinF-PCR2-Rep1_S132",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF2-BinF-PCR3-Rep1_S180",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF2-BinF-PCR4-Rep1_S186"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS1891GTLU/"
],
"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 F for 80-100% expression of FAM3C) 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": "2024-06-01T01:52:22.104712+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "5f53db00-426f-4ef1-8e8e-e1917ec16afa"
}