{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS3029MTKI/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS3029MTKI",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinF-PCR1_S78",
"jesse-engreitz:auxiliary_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinF-PCR2_S174",
"jesse-engreitz:auxiliary_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinF-PCR3_S270",
"jesse-engreitz:auxiliary_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinF-PCR4_S366"
],
"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 [IGVFDS3029MTKI](/auxiliary-sets/IGVFDS3029MTKI/) has sequence file(s) [IGVFFI6162BDDF](/sequence-files/IGVFFI6162BDDF/), [IGVFFI0939JLGV](/sequence-files/IGVFFI0939JLGV/), [IGVFFI3801VJQA](/sequence-files/IGVFFI3801VJQA/), [IGVFFI6403RRAQ](/sequence-files/IGVFFI6403RRAQ/) 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/IGVFDS3029MTKI/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS3029MTKI](/auxiliary-sets/IGVFDS3029MTKI/) 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/IGVFDS3029MTKI/"
}
]
},
"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": "2024-05-06T23:29:43.187174+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/IGVFFI6162BDDF/",
"accession": "IGVFFI6162BDDF",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinF-PCR1_S78"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:29:25.532695+00:00",
"file_format": "fastq",
"file_size": 2823910,
"href": "/sequence-files/IGVFFI6162BDDF/@@download/IGVFFI6162BDDF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/78c75c05-a774-45ee-a508-3cef2d39580e/IGVFFI6162BDDF.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/210301B002-CohesinFF/fastq/CCND1-Auxin0hrs-FF1-BinF-PCR1_S78_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5866GGCP/",
"accession": "IGVFFI5866GGCP",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinF-PCR1_S78"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:23:59.303294+00:00",
"file_format": "yaml",
"file_size": 907,
"href": "/configuration-files/IGVFFI5866GGCP/@@download/IGVFFI5866GGCP.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/070e3d7f-24c6-4f74-8b3d-455769a5d14a/IGVFFI5866GGCP.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin0hrs-FF1-BinF-PCR1_S78.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0939JLGV/",
"accession": "IGVFFI0939JLGV",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinF-PCR2_S174"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:29:41.334054+00:00",
"file_format": "fastq",
"file_size": 2754590,
"href": "/sequence-files/IGVFFI0939JLGV/@@download/IGVFFI0939JLGV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/b1a72dd0-952b-485b-87cd-048609254313/IGVFFI0939JLGV.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/210301B002-CohesinFF/fastq/CCND1-Auxin0hrs-FF1-BinF-PCR2_S174_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8008FYNH/",
"accession": "IGVFFI8008FYNH",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinF-PCR4_S366"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:24:39.130810+00:00",
"file_format": "yaml",
"file_size": 908,
"href": "/configuration-files/IGVFFI8008FYNH/@@download/IGVFFI8008FYNH.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/ad3030d3-262f-4044-8190-26ed4ca11aaf/IGVFFI8008FYNH.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin0hrs-FF1-BinF-PCR4_S366.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3801VJQA/",
"accession": "IGVFFI3801VJQA",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinF-PCR3_S270"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:29:58.181584+00:00",
"file_format": "fastq",
"file_size": 4111862,
"href": "/sequence-files/IGVFFI3801VJQA/@@download/IGVFFI3801VJQA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/e87f2da8-afda-4b4f-9693-62b7dc5dcc0e/IGVFFI3801VJQA.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/210301B002-CohesinFF/fastq/CCND1-Auxin0hrs-FF1-BinF-PCR3_S270_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6403RRAQ/",
"accession": "IGVFFI6403RRAQ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinF-PCR4_S366"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:30:14.502707+00:00",
"file_format": "fastq",
"file_size": 3642809,
"href": "/sequence-files/IGVFFI6403RRAQ/@@download/IGVFFI6403RRAQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/b9d74197-67f4-4325-b209-2be1ab145517/IGVFFI6403RRAQ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/210301B002-CohesinFF/fastq/CCND1-Auxin0hrs-FF1-BinF-PCR4_S366_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6703EYJY/",
"accession": "IGVFFI6703EYJY",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinF-PCR3_S270"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:24:25.818290+00:00",
"file_format": "yaml",
"file_size": 908,
"href": "/configuration-files/IGVFFI6703EYJY/@@download/IGVFFI6703EYJY.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/cb716eee-1d3b-4ad5-858e-e60b8a3b747e/IGVFFI6703EYJY.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin0hrs-FF1-BinF-PCR3_S270.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4141UFVD/",
"accession": "IGVFFI4141UFVD",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinF-PCR2_S174"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:24:12.523815+00:00",
"file_format": "yaml",
"file_size": 908,
"href": "/configuration-files/IGVFFI4141UFVD/@@download/IGVFFI4141UFVD.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/facdbd7d-9caf-4e45-9fee-a31ed36a00fd/IGVFFI4141UFVD.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin0hrs-FF1-BinF-PCR2_S174.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS4315AMOI/",
"accession": "IGVFDS4315AMOI",
"aliases": [
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinF-PCR1_S78",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinF-PCR2_S174",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinF-PCR3_S270",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinF-PCR4_S366"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:22:52.857660+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4674ZTIR/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4674ZTIR",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinF-PCR1_S78",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinF-PCR2_S174",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinF-PCR3_S270",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinF-PCR4_S366"
],
"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 F for 80-100% 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": "2024-06-01T01:29:25.532695+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in 36 genomic loci",
"uuid": "475560ba-7fb4-4163-bea4-b312afb733d9"
}