{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS5686BCWV/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS5686BCWV",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF2-BinD-PCR1-Rep1_S16",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF2-BinD-PCR2-Rep1_S22",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF2-BinD-PCR3-Rep1_S70",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF2-BinD-PCR4-Rep1_S76"
],
"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 [IGVFDS5686BCWV](/auxiliary-sets/IGVFDS5686BCWV/) has sequence file(s) [IGVFFI9405VYLM](/sequence-files/IGVFFI9405VYLM/), [IGVFFI0694FRDB](/sequence-files/IGVFFI0694FRDB/), [IGVFFI5037IDTR](/sequence-files/IGVFFI5037IDTR/), [IGVFFI3468FNAC](/sequence-files/IGVFFI3468FNAC/) 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/IGVFDS5686BCWV/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS5686BCWV](/auxiliary-sets/IGVFDS5686BCWV/) 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/IGVFDS5686BCWV/"
}
]
},
"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": "2024-05-14T20:31:21.040550+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/IGVFFI9405VYLM/",
"accession": "IGVFFI9405VYLM",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF2-BinD-PCR1-Rep1_S16"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:45:57.001817+00:00",
"file_format": "fastq",
"file_size": 9893485,
"href": "/sequence-files/IGVFFI9405VYLM/@@download/IGVFFI9405VYLM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/ec1954e0-5f4a-4323-b163-e5e961b13109/IGVFFI9405VYLM.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin0hrs-FF2-BinD-PCR1-Rep1_S16_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2268RIAK/",
"accession": "IGVFFI2268RIAK",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF2-BinD-PCR1-Rep1_S16"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:38:25.260747+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI2268RIAK/@@download/IGVFFI2268RIAK.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/04b6cbfc-63ef-45d1-9521-f8f7cbf8d4f2/IGVFFI2268RIAK.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF2-BinD-PCR1-Rep1_S16.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1293UJBT/",
"accession": "IGVFFI1293UJBT",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF2-BinD-PCR4-Rep1_S76"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:39:35.081047+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI1293UJBT/@@download/IGVFFI1293UJBT.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/97001486-35cf-4bd9-ab79-fe4963b58091/IGVFFI1293UJBT.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF2-BinD-PCR4-Rep1_S76.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0694FRDB/",
"accession": "IGVFFI0694FRDB",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF2-BinD-PCR2-Rep1_S22"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:46:20.261699+00:00",
"file_format": "fastq",
"file_size": 11230610,
"href": "/sequence-files/IGVFFI0694FRDB/@@download/IGVFFI0694FRDB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/d25b7f78-21d6-4470-a268-846689560eb0/IGVFFI0694FRDB.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin0hrs-FF2-BinD-PCR2-Rep1_S22_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5037IDTR/",
"accession": "IGVFFI5037IDTR",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF2-BinD-PCR3-Rep1_S70"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:46:38.044973+00:00",
"file_format": "fastq",
"file_size": 19549369,
"href": "/sequence-files/IGVFFI5037IDTR/@@download/IGVFFI5037IDTR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/d2e67756-1145-4771-b2ac-efd20f35b91d/IGVFFI5037IDTR.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin0hrs-FF2-BinD-PCR3-Rep1_S70_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3468FNAC/",
"accession": "IGVFFI3468FNAC",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF2-BinD-PCR4-Rep1_S76"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:46:55.904510+00:00",
"file_format": "fastq",
"file_size": 23927332,
"href": "/sequence-files/IGVFFI3468FNAC/@@download/IGVFFI3468FNAC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/8133d7a0-1d9e-48a7-850d-b8a8b7f811ab/IGVFFI3468FNAC.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin0hrs-FF2-BinD-PCR4-Rep1_S76_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2082IHRL/",
"accession": "IGVFFI2082IHRL",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF2-BinD-PCR2-Rep1_S22"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:38:41.016438+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI2082IHRL/@@download/IGVFFI2082IHRL.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/896592f4-a109-4ef2-9fa9-95b738b5f6cb/IGVFFI2082IHRL.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF2-BinD-PCR2-Rep1_S22.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2987ULMD/",
"accession": "IGVFFI2987ULMD",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF2-BinD-PCR3-Rep1_S70"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:39:19.579088+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI2987ULMD/@@download/IGVFFI2987ULMD.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/1a969a1a-6004-424e-8581-725ca4921220/IGVFFI2987ULMD.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF2-BinD-PCR3-Rep1_S70.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS5251YUKR/",
"accession": "IGVFDS5251YUKR",
"aliases": [
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF2-BinD-PCR1-Rep1_S16",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF2-BinD-PCR2-Rep1_S22",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF2-BinD-PCR3-Rep1_S70",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF2-BinD-PCR4-Rep1_S76"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:24:47.719907+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0599CFOW/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0599CFOW",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF2-BinD-PCR1-Rep1_S16",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF2-BinD-PCR2-Rep1_S22",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF2-BinD-PCR3-Rep1_S70",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF2-BinD-PCR4-Rep1_S76"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS5413RKIA/"
],
"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 SSFA2) 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": "2024-06-01T01:45:57.001817+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "d2c362f2-cd6c-45a0-a44d-50f8dff732f6"
}