{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS8183BLZH/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS8183BLZH",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF1-BinE-PCR1-Rep1_S5",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF1-BinE-PCR2-Rep1_S11",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF1-BinE-PCR3-Rep1_S59",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF1-BinE-PCR4-Rep1_S65"
],
"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 [IGVFDS8183BLZH](/auxiliary-sets/IGVFDS8183BLZH/) has sequence file(s) [IGVFFI2821MABS](/sequence-files/IGVFFI2821MABS/), [IGVFFI5991CNOJ](/sequence-files/IGVFFI5991CNOJ/), [IGVFFI6907NDCS](/sequence-files/IGVFFI6907NDCS/), [IGVFFI3035ARRF](/sequence-files/IGVFFI3035ARRF/) 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/IGVFDS8183BLZH/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS8183BLZH](/auxiliary-sets/IGVFDS8183BLZH/) 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/IGVFDS8183BLZH/"
}
]
},
"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": "2024-05-14T20:30:56.199465+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/IGVFFI2821MABS/",
"accession": "IGVFFI2821MABS",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF1-BinE-PCR1-Rep1_S5"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:44:47.399156+00:00",
"file_format": "fastq",
"file_size": 26662709,
"href": "/sequence-files/IGVFFI2821MABS/@@download/IGVFFI2821MABS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/fa9a4ace-784c-4bcf-b4cd-ee96c22bc7f8/IGVFFI2821MABS.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-BinE-PCR1-Rep1_S5_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7183VGSB/",
"accession": "IGVFFI7183VGSB",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF1-BinE-PCR1-Rep1_S5"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:37:26.623722+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI7183VGSB/@@download/IGVFFI7183VGSB.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/18875a9a-01bf-4ec1-ac0c-9e8b893ce0a6/IGVFFI7183VGSB.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF1-BinE-PCR1-Rep1_S5.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5991CNOJ/",
"accession": "IGVFFI5991CNOJ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF1-BinE-PCR2-Rep1_S11"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:45:06.159919+00:00",
"file_format": "fastq",
"file_size": 22193703,
"href": "/sequence-files/IGVFFI5991CNOJ/@@download/IGVFFI5991CNOJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/db22f8e8-5b39-43ab-bc41-b75d31aece90/IGVFFI5991CNOJ.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-BinE-PCR2-Rep1_S11_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6907NDCS/",
"accession": "IGVFFI6907NDCS",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF1-BinE-PCR3-Rep1_S59"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:45:23.801065+00:00",
"file_format": "fastq",
"file_size": 27577169,
"href": "/sequence-files/IGVFFI6907NDCS/@@download/IGVFFI6907NDCS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/27db3ba5-d09c-4bd2-aee9-844c78c760da/IGVFFI6907NDCS.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-BinE-PCR3-Rep1_S59_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3035ARRF/",
"accession": "IGVFFI3035ARRF",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF1-BinE-PCR4-Rep1_S65"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:45:41.780902+00:00",
"file_format": "fastq",
"file_size": 23977966,
"href": "/sequence-files/IGVFFI3035ARRF/@@download/IGVFFI3035ARRF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/2b0a4f42-8fb1-4d7b-82c3-00414af6375b/IGVFFI3035ARRF.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-BinE-PCR4-Rep1_S65_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6958HDRB/",
"accession": "IGVFFI6958HDRB",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF1-BinE-PCR3-Rep1_S59"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:37:57.025910+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI6958HDRB/@@download/IGVFFI6958HDRB.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/fa243c43-cae1-4e4a-b0bf-b513dca9c5d7/IGVFFI6958HDRB.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF1-BinE-PCR3-Rep1_S59.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9942FRQQ/",
"accession": "IGVFFI9942FRQQ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF1-BinE-PCR4-Rep1_S65"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:38:12.428265+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI9942FRQQ/@@download/IGVFFI9942FRQQ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/a4ea4770-a7e1-4385-90be-d37fa85508df/IGVFFI9942FRQQ.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF1-BinE-PCR4-Rep1_S65.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8314MSZX/",
"accession": "IGVFFI8314MSZX",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF1-BinE-PCR2-Rep1_S11"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:37:41.310626+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI8314MSZX/@@download/IGVFFI8314MSZX.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/3bfc8098-513f-4224-afa6-bb43e9c63bdc/IGVFFI8314MSZX.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF1-BinE-PCR2-Rep1_S11.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS0884TWTU/",
"accession": "IGVFDS0884TWTU",
"aliases": [
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinE-PCR1-Rep1_S5",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinE-PCR2-Rep1_S11",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinE-PCR3-Rep1_S59",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinE-PCR4-Rep1_S65"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:24:11.289221+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7435FSSP/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7435FSSP",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinE-PCR1-Rep1_S5",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinE-PCR2-Rep1_S11",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinE-PCR3-Rep1_S59",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinE-PCR4-Rep1_S65"
],
"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 E for 80-90% 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": "2024-06-01T01:44:47.399156+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "5076e4c8-dede-4144-981e-19e6f1f8e0bc"
}