{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS5675MHUS/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS5675MHUS",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF2-BinD-PCR1-Rep1_S124",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF2-BinD-PCR2-Rep1_S130",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF2-BinD-PCR3-Rep1_S178",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF2-BinD-PCR4-Rep1_S184"
],
"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 [IGVFDS5675MHUS](/auxiliary-sets/IGVFDS5675MHUS/) has sequence file(s) [IGVFFI8597VYJU](/sequence-files/IGVFFI8597VYJU/), [IGVFFI0373YORO](/sequence-files/IGVFFI0373YORO/), [IGVFFI4287HCJU](/sequence-files/IGVFFI4287HCJU/), [IGVFFI7926SPBK](/sequence-files/IGVFFI7926SPBK/) 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/IGVFDS5675MHUS/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS5675MHUS](/auxiliary-sets/IGVFDS5675MHUS/) 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/IGVFDS5675MHUS/"
}
]
},
"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": "2024-05-14T16:24:22.174180+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/IGVFFI8597VYJU/",
"accession": "IGVFFI8597VYJU",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF2-BinD-PCR1-Rep1_S124"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:52:16.243482+00:00",
"file_format": "fastq",
"file_size": 23768552,
"href": "/sequence-files/IGVFFI8597VYJU/@@download/IGVFFI8597VYJU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/dfa45282-1f3d-4b22-824e-d6e8696f0558/IGVFFI8597VYJU.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-BinD-PCR1-Rep1_S124_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7940UOBI/",
"accession": "IGVFFI7940UOBI",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF2-BinD-PCR1-Rep1_S124"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:42:53.157858+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI7940UOBI/@@download/IGVFFI7940UOBI.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/44aa4f54-4f71-4087-ac17-93b46f059102/IGVFFI7940UOBI.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF2-BinD-PCR1-Rep1_S124.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0373YORO/",
"accession": "IGVFFI0373YORO",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF2-BinD-PCR2-Rep1_S130"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:52:34.018365+00:00",
"file_format": "fastq",
"file_size": 23437372,
"href": "/sequence-files/IGVFFI0373YORO/@@download/IGVFFI0373YORO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/55bd388c-a640-4ea8-9f46-1a53592b9a56/IGVFFI0373YORO.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-BinD-PCR2-Rep1_S130_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4287HCJU/",
"accession": "IGVFFI4287HCJU",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF2-BinD-PCR3-Rep1_S178"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:52:52.381866+00:00",
"file_format": "fastq",
"file_size": 32929762,
"href": "/sequence-files/IGVFFI4287HCJU/@@download/IGVFFI4287HCJU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/990d8a43-ee13-4bd8-9b16-99a9e003ad71/IGVFFI4287HCJU.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-BinD-PCR3-Rep1_S178_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7926SPBK/",
"accession": "IGVFFI7926SPBK",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF2-BinD-PCR4-Rep1_S184"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:53:10.393973+00:00",
"file_format": "fastq",
"file_size": 35216637,
"href": "/sequence-files/IGVFFI7926SPBK/@@download/IGVFFI7926SPBK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/fafde862-bed5-44fb-8bc2-5cfb8612577f/IGVFFI7926SPBK.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-BinD-PCR4-Rep1_S184_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1867PKWL/",
"accession": "IGVFFI1867PKWL",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF2-BinD-PCR2-Rep1_S130"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:43:06.899323+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI1867PKWL/@@download/IGVFFI1867PKWL.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/8eabee1f-c0fd-48f8-9a8b-90f66dbc327c/IGVFFI1867PKWL.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF2-BinD-PCR2-Rep1_S130.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9134XSQU/",
"accession": "IGVFFI9134XSQU",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF2-BinD-PCR3-Rep1_S178"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:43:21.005310+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI9134XSQU/@@download/IGVFFI9134XSQU.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/9afd181f-bd31-482b-91ef-a3b463b200ec/IGVFFI9134XSQU.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF2-BinD-PCR3-Rep1_S178.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9099WRSF/",
"accession": "IGVFFI9099WRSF",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF2-BinD-PCR4-Rep1_S184"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:43:34.301011+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI9099WRSF/@@download/IGVFFI9099WRSF.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/1a81be6e-4613-4146-9c8d-f7631c0b9eaf/IGVFFI9099WRSF.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF2-BinD-PCR4-Rep1_S184.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS9829XFGT/",
"accession": "IGVFDS9829XFGT",
"aliases": [
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF2-BinD-PCR1-Rep1_S124",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF2-BinD-PCR2-Rep1_S130",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF2-BinD-PCR3-Rep1_S178",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF2-BinD-PCR4-Rep1_S184"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:11:43.284161+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8987EBZC/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8987EBZC",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF2-BinD-PCR1-Rep1_S124",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF2-BinD-PCR2-Rep1_S130",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF2-BinD-PCR3-Rep1_S178",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF2-BinD-PCR4-Rep1_S184"
],
"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 D for 55-65% 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": "2024-06-01T01:52:16.243482+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "ad0313eb-b5f6-4e6c-a03c-acc9d7cf6ca0"
}