{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS8492ZWVD/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS8492ZWVD",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF2-BinB-PCR1-Rep1_S230",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF2-BinB-PCR2-Rep1_S236",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF2-BinB-PCR3-Rep1_S272",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF2-BinB-PCR4-Rep1_S278"
],
"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 [IGVFDS8492ZWVD](/auxiliary-sets/IGVFDS8492ZWVD/) has sequence file(s) [IGVFFI9565FZNZ](/sequence-files/IGVFFI9565FZNZ/), [IGVFFI6852PRDQ](/sequence-files/IGVFFI6852PRDQ/), [IGVFFI9062PSUL](/sequence-files/IGVFFI9062PSUL/), [IGVFFI1218OAIH](/sequence-files/IGVFFI1218OAIH/) 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/IGVFDS8492ZWVD/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS8492ZWVD](/auxiliary-sets/IGVFDS8492ZWVD/) 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/IGVFDS8492ZWVD/"
}
]
},
"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": "2024-05-13T22:39:13.252806+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/IGVFFI9565FZNZ/",
"accession": "IGVFFI9565FZNZ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF2-BinB-PCR1-Rep1_S230"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:37:11.457096+00:00",
"file_format": "fastq",
"file_size": 24958082,
"href": "/sequence-files/IGVFFI9565FZNZ/@@download/IGVFFI9565FZNZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/d5bdc1a2-c59b-4b72-b6ac-313dfeae1621/IGVFFI9565FZNZ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin0hrs-FF2-BinB-PCR1-Rep1_S230_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1876ABOL/",
"accession": "IGVFFI1876ABOL",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF2-BinB-PCR1-Rep1_S230"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:28:58.509236+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI1876ABOL/@@download/IGVFFI1876ABOL.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/106f2e62-0b84-4c32-bda7-e2125f448903/IGVFFI1876ABOL.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF2-BinB-PCR1-Rep1_S230.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6852PRDQ/",
"accession": "IGVFFI6852PRDQ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF2-BinB-PCR2-Rep1_S236"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:37:29.546554+00:00",
"file_format": "fastq",
"file_size": 18602238,
"href": "/sequence-files/IGVFFI6852PRDQ/@@download/IGVFFI6852PRDQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/3aee977e-8eb0-447f-9d7f-d562dc83d26e/IGVFFI6852PRDQ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin0hrs-FF2-BinB-PCR2-Rep1_S236_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9062PSUL/",
"accession": "IGVFFI9062PSUL",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF2-BinB-PCR3-Rep1_S272"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:37:47.086105+00:00",
"file_format": "fastq",
"file_size": 27474093,
"href": "/sequence-files/IGVFFI9062PSUL/@@download/IGVFFI9062PSUL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/652e9561-b44b-44e4-9ee3-99c1f2e5f0a6/IGVFFI9062PSUL.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin0hrs-FF2-BinB-PCR3-Rep1_S272_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1218OAIH/",
"accession": "IGVFFI1218OAIH",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF2-BinB-PCR4-Rep1_S278"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:38:05.716965+00:00",
"file_format": "fastq",
"file_size": 19641540,
"href": "/sequence-files/IGVFFI1218OAIH/@@download/IGVFFI1218OAIH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/b49678e0-ee3f-4cf0-91d3-722b15151e00/IGVFFI1218OAIH.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin0hrs-FF2-BinB-PCR4-Rep1_S278_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5903GHCI/",
"accession": "IGVFFI5903GHCI",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF2-BinB-PCR3-Rep1_S272"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:29:26.612999+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI5903GHCI/@@download/IGVFFI5903GHCI.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/c08387b3-f864-47e2-b34b-ee9b499a6035/IGVFFI5903GHCI.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF2-BinB-PCR3-Rep1_S272.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3347MQPE/",
"accession": "IGVFFI3347MQPE",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF2-BinB-PCR4-Rep1_S278"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:29:40.605284+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI3347MQPE/@@download/IGVFFI3347MQPE.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/41dd722d-d76b-47c8-a9b5-10de4670d312/IGVFFI3347MQPE.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF2-BinB-PCR4-Rep1_S278.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9158EPYH/",
"accession": "IGVFFI9158EPYH",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF2-BinB-PCR2-Rep1_S236"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:29:12.774331+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI9158EPYH/@@download/IGVFFI9158EPYH.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/0b0fe4cd-2941-4cea-9ef6-28aa4af27ecc/IGVFFI9158EPYH.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF2-BinB-PCR2-Rep1_S236.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS3149HCGU/",
"accession": "IGVFDS3149HCGU",
"aliases": [
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF2-BinB-PCR1-Rep1_S230",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF2-BinB-PCR2-Rep1_S236",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF2-BinB-PCR3-Rep1_S272",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF2-BinB-PCR4-Rep1_S278"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:08:37.730861+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM6482UHDK/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6482UHDK",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF2-BinB-PCR1-Rep1_S230",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF2-BinB-PCR2-Rep1_S236",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF2-BinB-PCR3-Rep1_S272",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF2-BinB-PCR4-Rep1_S278"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS6351FGNG/"
],
"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 B for 10-20% 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": "2024-06-01T01:37:11.457096+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "6f59ed53-bc21-412d-8d66-15aed8cfdb8e"
}