{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS1630KVRE/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS1630KVRE",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF1-BinC-PCR1_S51",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF1-BinC-PCR2_S57",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF1-BinC-PCR3_S147",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF1-BinC-PCR4_S153"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM0623GQRJ](/in-vitro-systems/IGVFSM0623GQRJ/) 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/IGVFSM0623GQRJ/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM0623GQRJ](/in-vitro-systems/IGVFSM0623GQRJ/) 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/IGVFSM0623GQRJ/"
},
{
"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 [IGVFDS1630KVRE](/auxiliary-sets/IGVFDS1630KVRE/) has sequence file(s) [IGVFFI7346SZCE](/sequence-files/IGVFFI7346SZCE/), [IGVFFI5577IRJO](/sequence-files/IGVFFI5577IRJO/), [IGVFFI0388ZLUI](/sequence-files/IGVFFI0388ZLUI/), [IGVFFI9213RYPE](/sequence-files/IGVFFI9213RYPE/) 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/IGVFDS1630KVRE/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS1630KVRE](/auxiliary-sets/IGVFDS1630KVRE/) 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/IGVFDS1630KVRE/"
}
]
},
"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": "2024-05-16T17:58:56.864201+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/IGVFFI7346SZCE/",
"accession": "IGVFFI7346SZCE",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF1-BinC-PCR1_S51"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:20:04.752128+00:00",
"file_format": "fastq",
"file_size": 10928677,
"href": "/sequence-files/IGVFFI7346SZCE/@@download/IGVFFI7346SZCE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/6d8ea55e-099b-4031-b2f0-688b3199cf77/IGVFFI7346SZCE.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF1-BinC-PCR1_S51_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7354GKJC/",
"accession": "IGVFFI7354GKJC",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF1-BinC-PCR1_S51"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:09:23.375059+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI7354GKJC/@@download/IGVFFI7354GKJC.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/5db77b50-4d12-49ed-a46b-701f3079f791/IGVFFI7354GKJC.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF1-BinC-PCR1_S51.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9887XTYA/",
"accession": "IGVFFI9887XTYA",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF1-BinC-PCR3_S147"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:09:53.678815+00:00",
"file_format": "yaml",
"file_size": 904,
"href": "/configuration-files/IGVFFI9887XTYA/@@download/IGVFFI9887XTYA.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/f624eff6-d508-4003-adad-071d7f9f2b84/IGVFFI9887XTYA.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF1-BinC-PCR3_S147.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5577IRJO/",
"accession": "IGVFFI5577IRJO",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF1-BinC-PCR4_S153"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:21:01.484356+00:00",
"file_format": "fastq",
"file_size": 17979334,
"href": "/sequence-files/IGVFFI5577IRJO/@@download/IGVFFI5577IRJO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/3f6bb7be-b343-4bb2-972c-af37334a8cda/IGVFFI5577IRJO.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF1-BinC-PCR4_S153_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6558VOZQ/",
"accession": "IGVFFI6558VOZQ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF1-BinC-PCR2_S57"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:09:38.822979+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI6558VOZQ/@@download/IGVFFI6558VOZQ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/b452b754-6de6-4848-bda7-a804b4bf2bc4/IGVFFI6558VOZQ.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF1-BinC-PCR2_S57.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0388ZLUI/",
"accession": "IGVFFI0388ZLUI",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF1-BinC-PCR2_S57"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:20:22.039881+00:00",
"file_format": "fastq",
"file_size": 8575302,
"href": "/sequence-files/IGVFFI0388ZLUI/@@download/IGVFFI0388ZLUI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/1afa776e-fe13-4db3-b6fa-44dbdfd98c45/IGVFFI0388ZLUI.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF1-BinC-PCR2_S57_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9213RYPE/",
"accession": "IGVFFI9213RYPE",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF1-BinC-PCR3_S147"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:20:43.450248+00:00",
"file_format": "fastq",
"file_size": 20544113,
"href": "/sequence-files/IGVFFI9213RYPE/@@download/IGVFFI9213RYPE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/8bc4e454-dc7f-4f2c-943b-1a0c2b35676f/IGVFFI9213RYPE.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF1-BinC-PCR3_S147_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1153OFSA/",
"accession": "IGVFFI1153OFSA",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF1-BinC-PCR4_S153"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:10:08.691617+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI1153OFSA/@@download/IGVFFI1153OFSA.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/cdde501f-f362-4076-a368-939054b3febc/IGVFFI1153OFSA.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF1-BinC-PCR4_S153.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS6407EOOV/",
"accession": "IGVFDS6407EOOV",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF1-BinC-PCR1_S51",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF1-BinC-PCR2_S57",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF1-BinC-PCR3_S147",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF1-BinC-PCR4_S153"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:16:34.431466+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0623GQRJ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0623GQRJ",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF1-BinC-PCR1_S51",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF1-BinC-PCR2_S57",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF1-BinC-PCR3_S147",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF1-BinC-PCR4_S153"
],
"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 C for 35-45% 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": "2024-06-01T02:20:04.752128+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "4a846d5c-5621-4833-827e-b491b3e45eee"
}