{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS4721YEEW/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS4721YEEW",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR1-Rep1_S17",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR2-Rep1_S23",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR3-Rep1_S71",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR4-Rep1_S77"
],
"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 [IGVFDS4721YEEW](/auxiliary-sets/IGVFDS4721YEEW/) has sequence file(s) [IGVFFI7752CYYJ](/sequence-files/IGVFFI7752CYYJ/), [IGVFFI4315EDNJ](/sequence-files/IGVFFI4315EDNJ/), [IGVFFI6094QETO](/sequence-files/IGVFFI6094QETO/), [IGVFFI8646GHGN](/sequence-files/IGVFFI8646GHGN/) 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/IGVFDS4721YEEW/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS4721YEEW](/auxiliary-sets/IGVFDS4721YEEW/) 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/IGVFDS4721YEEW/"
}
]
},
"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": "2024-05-14T20:31:21.906143+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/IGVFFI7752CYYJ/",
"accession": "IGVFFI7752CYYJ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR1-Rep1_S17"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:46:03.633426+00:00",
"file_format": "fastq",
"file_size": 9130239,
"href": "/sequence-files/IGVFFI7752CYYJ/@@download/IGVFFI7752CYYJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/f1725405-7e26-42d5-b449-13f52bea58cf/IGVFFI7752CYYJ.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-BinE-PCR1-Rep1_S17_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3316VTMT/",
"accession": "IGVFFI3316VTMT",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR1-Rep1_S17"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:38:28.029318+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI3316VTMT/@@download/IGVFFI3316VTMT.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/85fd1a9d-04d6-4a83-9ae4-9dbe29db0e20/IGVFFI3316VTMT.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF2-BinE-PCR1-Rep1_S17.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4315EDNJ/",
"accession": "IGVFFI4315EDNJ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR2-Rep1_S23"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:46:23.222743+00:00",
"file_format": "fastq",
"file_size": 19460589,
"href": "/sequence-files/IGVFFI4315EDNJ/@@download/IGVFFI4315EDNJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/3c140bbf-4f16-40be-be23-b5e996d0cbda/IGVFFI4315EDNJ.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-BinE-PCR2-Rep1_S23_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6094QETO/",
"accession": "IGVFFI6094QETO",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR3-Rep1_S71"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:46:40.966016+00:00",
"file_format": "fastq",
"file_size": 14344858,
"href": "/sequence-files/IGVFFI6094QETO/@@download/IGVFFI6094QETO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/3e20f801-835d-4a18-9032-209ef76b7075/IGVFFI6094QETO.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-BinE-PCR3-Rep1_S71_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8646GHGN/",
"accession": "IGVFFI8646GHGN",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR4-Rep1_S77"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:46:58.883877+00:00",
"file_format": "fastq",
"file_size": 20050660,
"href": "/sequence-files/IGVFFI8646GHGN/@@download/IGVFFI8646GHGN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/5523ffb8-5160-446b-963a-418279843f0b/IGVFFI8646GHGN.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-BinE-PCR4-Rep1_S77_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4784OLOD/",
"accession": "IGVFFI4784OLOD",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR3-Rep1_S71"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:39:22.214545+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI4784OLOD/@@download/IGVFFI4784OLOD.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/43cbe569-08db-4c7f-9ebb-95d2a903aa3d/IGVFFI4784OLOD.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF2-BinE-PCR3-Rep1_S71.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0392HWSG/",
"accession": "IGVFFI0392HWSG",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR4-Rep1_S77"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:39:38.091137+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI0392HWSG/@@download/IGVFFI0392HWSG.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/cf53b9cb-581f-4582-bbea-090e206a46b2/IGVFFI0392HWSG.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF2-BinE-PCR4-Rep1_S77.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5168BJYX/",
"accession": "IGVFFI5168BJYX",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR2-Rep1_S23"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:38:43.507832+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI5168BJYX/@@download/IGVFFI5168BJYX.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/ed0867b0-4f40-443f-8095-2a179f68bd71/IGVFFI5168BJYX.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF2-BinE-PCR2-Rep1_S23.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS8098OGBN/",
"accession": "IGVFDS8098OGBN",
"aliases": [
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR1-Rep1_S17",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR2-Rep1_S23",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR3-Rep1_S71",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR4-Rep1_S77"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:24:54.299714+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9097DRIA/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9097DRIA",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR1-Rep1_S17",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR2-Rep1_S23",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR3-Rep1_S71",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR4-Rep1_S77"
],
"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": "2024-06-01T01:46:03.633426+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "e1d0b00e-9916-4c5b-9451-df9e051ed838"
}