{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS9665KRGJ/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS9665KRGJ",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF4-BinB-PCR1_S86",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF4-BinB-PCR2_S92",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF4-BinB-PCR3_S182",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF4-BinB-PCR4_S188"
],
"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 [IGVFSM5182LFZS](/in-vitro-systems/IGVFSM5182LFZS/) 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/IGVFSM5182LFZS/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM5182LFZS](/in-vitro-systems/IGVFSM5182LFZS/) 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/IGVFSM5182LFZS/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS9665KRGJ](/auxiliary-sets/IGVFDS9665KRGJ/) has sequence file(s) [IGVFFI8664EIWJ](/sequence-files/IGVFFI8664EIWJ/), [IGVFFI7849AHAB](/sequence-files/IGVFFI7849AHAB/), [IGVFFI3502JPZE](/sequence-files/IGVFFI3502JPZE/), [IGVFFI9283IUBN](/sequence-files/IGVFFI9283IUBN/) 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/IGVFDS9665KRGJ/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS9665KRGJ](/auxiliary-sets/IGVFDS9665KRGJ/) 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/IGVFDS9665KRGJ/"
}
]
},
"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": "2024-05-16T18:01:20.088784+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/IGVFFI8664EIWJ/",
"accession": "IGVFFI8664EIWJ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF4-BinB-PCR1_S86"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T15:27:53.904045+00:00",
"file_format": "fastq",
"file_size": 7015668,
"href": "/sequence-files/IGVFFI8664EIWJ/@@download/IGVFFI8664EIWJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/e5ee4791-c736-470a-a434-fe33e2e5e494/IGVFFI8664EIWJ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF4-BinB-PCR1_S86_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2146QZKY/",
"accession": "IGVFFI2146QZKY",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF4-BinB-PCR1_S86"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:12:19.546139+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI2146QZKY/@@download/IGVFFI2146QZKY.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/60e4346c-b63d-440b-94a1-e7b6d08a8296/IGVFFI2146QZKY.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF4-BinB-PCR1_S86.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7849AHAB/",
"accession": "IGVFFI7849AHAB",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF4-BinB-PCR2_S92"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T15:28:09.762574+00:00",
"file_format": "fastq",
"file_size": 4290605,
"href": "/sequence-files/IGVFFI7849AHAB/@@download/IGVFFI7849AHAB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/006c0460-dd89-4347-a972-86f7478bf9ac/IGVFFI7849AHAB.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF4-BinB-PCR2_S92_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3502JPZE/",
"accession": "IGVFFI3502JPZE",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF4-BinB-PCR3_S182"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T15:28:25.961215+00:00",
"file_format": "fastq",
"file_size": 11929855,
"href": "/sequence-files/IGVFFI3502JPZE/@@download/IGVFFI3502JPZE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/0070e984-e509-4452-9fb9-709bad8eee4a/IGVFFI3502JPZE.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF4-BinB-PCR3_S182_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5599GUUW/",
"accession": "IGVFFI5599GUUW",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF4-BinB-PCR2_S92"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:12:34.058352+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI5599GUUW/@@download/IGVFFI5599GUUW.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/b2bd19c0-dbb4-4485-bc18-5d432670ccee/IGVFFI5599GUUW.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF4-BinB-PCR2_S92.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9283IUBN/",
"accession": "IGVFFI9283IUBN",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF4-BinB-PCR4_S188"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T15:28:42.415136+00:00",
"file_format": "fastq",
"file_size": 9036588,
"href": "/sequence-files/IGVFFI9283IUBN/@@download/IGVFFI9283IUBN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/aa553202-7028-4d64-887a-a9e6f35ab1ce/IGVFFI9283IUBN.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF4-BinB-PCR4_S188_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2941VKHY/",
"accession": "IGVFFI2941VKHY",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF4-BinB-PCR4_S188"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:13:03.582219+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI2941VKHY/@@download/IGVFFI2941VKHY.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/79e1e338-b2ec-4bcf-ab52-6f4573d28d48/IGVFFI2941VKHY.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF4-BinB-PCR4_S188.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7128OXNM/",
"accession": "IGVFFI7128OXNM",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF4-BinB-PCR3_S182"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:12:48.789391+00:00",
"file_format": "yaml",
"file_size": 904,
"href": "/configuration-files/IGVFFI7128OXNM/@@download/IGVFFI7128OXNM.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/52d26be3-fcad-42eb-9575-45cbef66bcd0/IGVFFI7128OXNM.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF4-BinB-PCR3_S182.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS2273HBVA/",
"accession": "IGVFDS2273HBVA",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF4-BinB-PCR1_S86",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF4-BinB-PCR2_S92",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF4-BinB-PCR3_S182",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF4-BinB-PCR4_S188"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:18:37.215309+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5182LFZS/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5182LFZS",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF4-BinB-PCR1_S86",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF4-BinB-PCR2_S92",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF4-BinB-PCR3_S182",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF4-BinB-PCR4_S188"
],
"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 B for 10-20% 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": "2024-06-03T15:27:53.904045+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "31b37085-0564-49b2-9960-6c5576f8a90d"
}