{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS1369IMLU/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS1369IMLU",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR1-Rep1_S6",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR2-Rep1_S12",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR3-Rep1_S60",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR4-Rep1_S66"
],
"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 [IGVFDS1369IMLU](/auxiliary-sets/IGVFDS1369IMLU/) has sequence file(s) [IGVFFI1019WGYS](/sequence-files/IGVFFI1019WGYS/), [IGVFFI8263MWWS](/sequence-files/IGVFFI8263MWWS/), [IGVFFI3575WNTZ](/sequence-files/IGVFFI3575WNTZ/), [IGVFFI9696NSTM](/sequence-files/IGVFFI9696NSTM/) 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/IGVFDS1369IMLU/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS1369IMLU](/auxiliary-sets/IGVFDS1369IMLU/) 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/IGVFDS1369IMLU/"
}
]
},
"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": "2024-05-14T20:30:56.982423+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/IGVFFI1019WGYS/",
"accession": "IGVFFI1019WGYS",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR1-Rep1_S6"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:44:50.372423+00:00",
"file_format": "fastq",
"file_size": 29169256,
"href": "/sequence-files/IGVFFI1019WGYS/@@download/IGVFFI1019WGYS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/6a0ef93b-d83f-43b4-84e3-f59c08f4fed4/IGVFFI1019WGYS.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-BinF-PCR1-Rep1_S6_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5738MQSZ/",
"accession": "IGVFFI5738MQSZ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR1-Rep1_S6"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:37:29.158263+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI5738MQSZ/@@download/IGVFFI5738MQSZ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/f7f901d8-d2e9-42c6-82d0-51f2cce9a8b0/IGVFFI5738MQSZ.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF1-BinF-PCR1-Rep1_S6.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8263MWWS/",
"accession": "IGVFFI8263MWWS",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR2-Rep1_S12"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:45:09.229837+00:00",
"file_format": "fastq",
"file_size": 35207176,
"href": "/sequence-files/IGVFFI8263MWWS/@@download/IGVFFI8263MWWS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/bd0e67cf-a11f-413e-8b04-c75912dd7f59/IGVFFI8263MWWS.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-BinF-PCR2-Rep1_S12_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3575WNTZ/",
"accession": "IGVFFI3575WNTZ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR3-Rep1_S60"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:45:26.802479+00:00",
"file_format": "fastq",
"file_size": 27117255,
"href": "/sequence-files/IGVFFI3575WNTZ/@@download/IGVFFI3575WNTZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/3aeb7dac-ca1b-42a4-9d93-933052b2d191/IGVFFI3575WNTZ.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-BinF-PCR3-Rep1_S60_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9696NSTM/",
"accession": "IGVFFI9696NSTM",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR4-Rep1_S66"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:45:44.683382+00:00",
"file_format": "fastq",
"file_size": 24887465,
"href": "/sequence-files/IGVFFI9696NSTM/@@download/IGVFFI9696NSTM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/e87543cb-09a8-41be-9333-8f0db40080d6/IGVFFI9696NSTM.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-BinF-PCR4-Rep1_S66_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8013LHCK/",
"accession": "IGVFFI8013LHCK",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR3-Rep1_S60"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:37:59.510511+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI8013LHCK/@@download/IGVFFI8013LHCK.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/3dcfa6d0-8d12-4599-ad28-bd5a6a274728/IGVFFI8013LHCK.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF1-BinF-PCR3-Rep1_S60.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3817IEYP/",
"accession": "IGVFFI3817IEYP",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR4-Rep1_S66"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:38:15.142296+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI3817IEYP/@@download/IGVFFI3817IEYP.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/00f9a3e6-6de5-4623-a80e-7ececd0a32cc/IGVFFI3817IEYP.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF1-BinF-PCR4-Rep1_S66.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5161XQVK/",
"accession": "IGVFFI5161XQVK",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR2-Rep1_S12"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:37:44.068688+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI5161XQVK/@@download/IGVFFI5161XQVK.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/62ede40d-3c8a-440b-a003-7570bfc03728/IGVFFI5161XQVK.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF1-BinF-PCR2-Rep1_S12.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS0674KOZU/",
"accession": "IGVFDS0674KOZU",
"aliases": [
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR1-Rep1_S6",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR2-Rep1_S12",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR3-Rep1_S60",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR4-Rep1_S66"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:24:18.378086+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4326ZGNE/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4326ZGNE",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR1-Rep1_S6",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR2-Rep1_S12",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR3-Rep1_S60",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR4-Rep1_S66"
],
"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 F for 80-100% 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": "2024-06-01T01:44:50.372423+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "c3dea016-4963-4c35-aaaf-07e383b1418e"
}