{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS7928JRLY/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS7928JRLY",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF2-BinA-PCR1_S61",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF2-BinA-PCR2_S67",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF2-BinA-PCR3_S157",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF2-BinA-PCR4_S163"
],
"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/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM8085CGHV](/in-vitro-systems/IGVFSM8085CGHV/) has in progress subobject degron modification [95081d1b-08b4-49ed-b324-e53fc43d8456](/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM8085CGHV/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM8085CGHV](/in-vitro-systems/IGVFSM8085CGHV/) has in progress subobject treatment [d35868d1-c45b-49ae-8ff3-a9c0c22551c2](/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM8085CGHV/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS7928JRLY](/auxiliary-sets/IGVFDS7928JRLY/) has sequence file(s) [IGVFFI4782QJVA](/sequence-files/IGVFFI4782QJVA/), [IGVFFI0997LMOA](/sequence-files/IGVFFI0997LMOA/), [IGVFFI4625BMCS](/sequence-files/IGVFFI4625BMCS/), [IGVFFI7283SWVN](/sequence-files/IGVFFI7283SWVN/) 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/IGVFDS7928JRLY/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS7928JRLY](/auxiliary-sets/IGVFDS7928JRLY/) 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/IGVFDS7928JRLY/"
}
]
},
"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": "2024-05-16T17:59:34.868318+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/IGVFFI4782QJVA/",
"accession": "IGVFFI4782QJVA",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF2-BinA-PCR1_S61"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T15:22:25.922961+00:00",
"file_format": "fastq",
"file_size": 22242207,
"href": "/sequence-files/IGVFFI4782QJVA/@@download/IGVFFI4782QJVA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/6e614558-f9fb-4fd6-8e98-fa8947e993b0/IGVFFI4782QJVA.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF2-BinA-PCR1_S61_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0959LGYD/",
"accession": "IGVFFI0959LGYD",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF2-BinA-PCR1_S61"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:10:18.188771+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI0959LGYD/@@download/IGVFFI0959LGYD.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/46c97bf5-4654-41a9-950f-43680b706ab1/IGVFFI0959LGYD.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF2-BinA-PCR1_S61.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0997LMOA/",
"accession": "IGVFFI0997LMOA",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF2-BinA-PCR2_S67"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T15:22:43.030974+00:00",
"file_format": "fastq",
"file_size": 9029343,
"href": "/sequence-files/IGVFFI0997LMOA/@@download/IGVFFI0997LMOA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/ce9d94eb-afce-48a4-962d-e4fbef46fe4c/IGVFFI0997LMOA.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF2-BinA-PCR2_S67_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4625BMCS/",
"accession": "IGVFFI4625BMCS",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF2-BinA-PCR3_S157"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T15:26:06.444502+00:00",
"file_format": "fastq",
"file_size": 40971037,
"href": "/sequence-files/IGVFFI4625BMCS/@@download/IGVFFI4625BMCS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/bb9bbd01-2aa1-4873-9ba4-bfff433c072d/IGVFFI4625BMCS.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF2-BinA-PCR3_S157_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7283SWVN/",
"accession": "IGVFFI7283SWVN",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF2-BinA-PCR4_S163"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T15:26:27.375980+00:00",
"file_format": "fastq",
"file_size": 18618625,
"href": "/sequence-files/IGVFFI7283SWVN/@@download/IGVFFI7283SWVN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/71d4c38d-50ea-49aa-b68a-9fd20beaf7d5/IGVFFI7283SWVN.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF2-BinA-PCR4_S163_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0920UKZB/",
"accession": "IGVFFI0920UKZB",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF2-BinA-PCR4_S163"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:11:05.013184+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI0920UKZB/@@download/IGVFFI0920UKZB.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/1b0f36bb-e24d-4c15-a2b0-16deca0c9d05/IGVFFI0920UKZB.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF2-BinA-PCR4_S163.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3220MAND/",
"accession": "IGVFFI3220MAND",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF2-BinA-PCR2_S67"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:10:33.236478+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI3220MAND/@@download/IGVFFI3220MAND.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/28a21c49-e3ed-4ff8-85b6-c9d5d204c608/IGVFFI3220MAND.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF2-BinA-PCR2_S67.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8082BFNJ/",
"accession": "IGVFFI8082BFNJ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF2-BinA-PCR3_S157"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:10:48.053295+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI8082BFNJ/@@download/IGVFFI8082BFNJ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/87765a47-21c4-4605-8dc6-4f7920474b04/IGVFFI8082BFNJ.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF2-BinA-PCR3_S157.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS9772ARQM/",
"accession": "IGVFDS9772ARQM",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF2-BinA-PCR1_S61",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF2-BinA-PCR2_S67",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF2-BinA-PCR3_S157",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF2-BinA-PCR4_S163"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"notes": "This dataset originally had the alias jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF2-BinB-PCR3_S157 but it was changed to jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF2-BinA-PCR3_S157.",
"release_timestamp": "2024-07-10T20:17:04.536503+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8085CGHV/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8085CGHV",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF2-BinA-PCR1_S61",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF2-BinA-PCR2_S67",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF2-BinA-PCR3_S157",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF2-BinA-PCR4_S163"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS7846UISG/"
],
"modifications": [
"/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/",
"/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 A for 0-10% expression of KITLG) treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours, modified with a guide library",
"taxa": "Homo sapiens",
"treatments": [
"/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/"
]
}
],
"schema_version": "11",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-03T15:22:25.922961+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "a802e8e5-f06a-4587-a440-4ceeb7f76476"
}