{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS0241XMRI/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS0241XMRI",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF1-BinD-PCR1-Rep1_S4",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF1-BinD-PCR2-Rep1_S10",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF1-BinD-PCR3-Rep1_S58",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF1-BinD-PCR4-Rep1_S64"
],
"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 [IGVFDS0241XMRI](/auxiliary-sets/IGVFDS0241XMRI/) has sequence file(s) [IGVFFI5037ZQHU](/sequence-files/IGVFFI5037ZQHU/), [IGVFFI0621LSOC](/sequence-files/IGVFFI0621LSOC/), [IGVFFI6991LZWF](/sequence-files/IGVFFI6991LZWF/), [IGVFFI6147WPCX](/sequence-files/IGVFFI6147WPCX/) 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/IGVFDS0241XMRI/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS0241XMRI](/auxiliary-sets/IGVFDS0241XMRI/) 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/IGVFDS0241XMRI/"
}
]
},
"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": "2024-05-14T20:30:55.440211+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/IGVFFI5037ZQHU/",
"accession": "IGVFFI5037ZQHU",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF1-BinD-PCR1-Rep1_S4"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:44:44.451017+00:00",
"file_format": "fastq",
"file_size": 6850184,
"href": "/sequence-files/IGVFFI5037ZQHU/@@download/IGVFFI5037ZQHU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/6f1e0f19-03b8-42e9-932e-90beca84db64/IGVFFI5037ZQHU.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-FF1-BinD-PCR1-Rep1_S4_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0566CKPJ/",
"accession": "IGVFFI0566CKPJ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF1-BinD-PCR1-Rep1_S4"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:37:24.308232+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI0566CKPJ/@@download/IGVFFI0566CKPJ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/b2867c65-688d-4952-b116-8cff93986f84/IGVFFI0566CKPJ.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF1-BinD-PCR1-Rep1_S4.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0621LSOC/",
"accession": "IGVFFI0621LSOC",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF1-BinD-PCR3-Rep1_S58"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:45:20.782784+00:00",
"file_format": "fastq",
"file_size": 10270135,
"href": "/sequence-files/IGVFFI0621LSOC/@@download/IGVFFI0621LSOC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/90e3c3f6-a23b-444e-adcb-5414c7b9863f/IGVFFI0621LSOC.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-FF1-BinD-PCR3-Rep1_S58_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7183LNMQ/",
"accession": "IGVFFI7183LNMQ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF1-BinD-PCR3-Rep1_S58"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:37:54.406379+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI7183LNMQ/@@download/IGVFFI7183LNMQ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/f8f0db89-55a3-40a9-8a7a-0d9d867fc120/IGVFFI7183LNMQ.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF1-BinD-PCR3-Rep1_S58.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6991LZWF/",
"accession": "IGVFFI6991LZWF",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF1-BinD-PCR2-Rep1_S10"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:45:03.419803+00:00",
"file_format": "fastq",
"file_size": 7043597,
"href": "/sequence-files/IGVFFI6991LZWF/@@download/IGVFFI6991LZWF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/d32a906a-e85c-4daf-a321-a110fae60587/IGVFFI6991LZWF.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-FF1-BinD-PCR2-Rep1_S10_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6147WPCX/",
"accession": "IGVFFI6147WPCX",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF1-BinD-PCR4-Rep1_S64"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:45:38.833879+00:00",
"file_format": "fastq",
"file_size": 14757260,
"href": "/sequence-files/IGVFFI6147WPCX/@@download/IGVFFI6147WPCX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/e0d37963-0115-4ed3-8ebb-aacd973cb2b0/IGVFFI6147WPCX.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-FF1-BinD-PCR4-Rep1_S64_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5999FTUB/",
"accession": "IGVFFI5999FTUB",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF1-BinD-PCR4-Rep1_S64"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:38:09.823794+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI5999FTUB/@@download/IGVFFI5999FTUB.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/2a75c8b3-d34a-4994-b09f-172235671887/IGVFFI5999FTUB.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF1-BinD-PCR4-Rep1_S64.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4956UORA/",
"accession": "IGVFFI4956UORA",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF1-BinD-PCR2-Rep1_S10"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:37:38.740871+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI4956UORA/@@download/IGVFFI4956UORA.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/3e229ff2-e583-49ea-bbc2-60570c5139d4/IGVFFI4956UORA.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF1-BinD-PCR2-Rep1_S10.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS1338GOGT/",
"accession": "IGVFDS1338GOGT",
"aliases": [
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinD-PCR1-Rep1_S4",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinD-PCR2-Rep1_S10",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinD-PCR3-Rep1_S58",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinD-PCR4-Rep1_S64"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:24:03.655488+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5613UEVU/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5613UEVU",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinD-PCR1-Rep1_S4",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinD-PCR2-Rep1_S10",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinD-PCR3-Rep1_S58",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinD-PCR4-Rep1_S64"
],
"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": "2024-06-01T01:44:44.451017+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "fa85b865-894b-4c64-9bb4-e3947b38c9bc"
}