{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS0051MRCH/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS0051MRCH",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR1-Rep1_S242",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR2-Rep1_S248",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR3-Rep1_S284",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR4-Rep1_S290"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM5255ABUW](/in-vitro-systems/IGVFSM5255ABUW/) 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/IGVFSM5255ABUW/"
},
{
"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/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS0051MRCH](/auxiliary-sets/IGVFDS0051MRCH/) has sequence file(s) [IGVFFI4348ZUXP](/sequence-files/IGVFFI4348ZUXP/), [IGVFFI0056ZWFB](/sequence-files/IGVFFI0056ZWFB/), [IGVFFI1781YSJE](/sequence-files/IGVFFI1781YSJE/), [IGVFFI8211KHIX](/sequence-files/IGVFFI8211KHIX/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS0051MRCH/"
}
]
},
"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": "2024-05-13T22:50:43.949177+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/IGVFFI4348ZUXP/",
"accession": "IGVFFI4348ZUXP",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR1-Rep1_S242"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:42:03.750959+00:00",
"file_format": "fastq",
"file_size": 21187778,
"href": "/sequence-files/IGVFFI4348ZUXP/@@download/IGVFFI4348ZUXP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/918f39a3-4639-47fb-a14e-4729d40df862/IGVFFI4348ZUXP.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin6hrs-FF1-BinB-PCR1-Rep1_S242_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6541RIBO/",
"accession": "IGVFFI6541RIBO",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR1-Rep1_S242"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:29:54.459004+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI6541RIBO/@@download/IGVFFI6541RIBO.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/8eee4e1c-1f92-412c-acb1-2a58e5765bd8/IGVFFI6541RIBO.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF1-BinB-PCR1-Rep1_S242.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0056ZWFB/",
"accession": "IGVFFI0056ZWFB",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR2-Rep1_S248"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:42:21.490730+00:00",
"file_format": "fastq",
"file_size": 15476191,
"href": "/sequence-files/IGVFFI0056ZWFB/@@download/IGVFFI0056ZWFB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/3f8af430-a4cd-4b6f-9ac6-caca93fce82b/IGVFFI0056ZWFB.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin6hrs-FF1-BinB-PCR2-Rep1_S248_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1781YSJE/",
"accession": "IGVFFI1781YSJE",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR3-Rep1_S284"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:42:38.091546+00:00",
"file_format": "fastq",
"file_size": 33923038,
"href": "/sequence-files/IGVFFI1781YSJE/@@download/IGVFFI1781YSJE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/3541381a-a7d4-4405-8ea4-244223aee743/IGVFFI1781YSJE.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin6hrs-FF1-BinB-PCR3-Rep1_S284_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8211KHIX/",
"accession": "IGVFFI8211KHIX",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR4-Rep1_S290"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:42:55.899195+00:00",
"file_format": "fastq",
"file_size": 23445132,
"href": "/sequence-files/IGVFFI8211KHIX/@@download/IGVFFI8211KHIX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/d540256b-ab1d-4792-b9c0-5388c9cd4df6/IGVFFI8211KHIX.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin6hrs-FF1-BinB-PCR4-Rep1_S290_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8434JLTQ/",
"accession": "IGVFFI8434JLTQ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR2-Rep1_S248"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:30:08.700092+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI8434JLTQ/@@download/IGVFFI8434JLTQ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/43656b07-a9ab-4829-af23-2074e998d577/IGVFFI8434JLTQ.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF1-BinB-PCR2-Rep1_S248.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4045SHGK/",
"accession": "IGVFFI4045SHGK",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR3-Rep1_S284"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:30:22.769115+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI4045SHGK/@@download/IGVFFI4045SHGK.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/5966239d-b340-48b5-bb4a-e74b887e9bdd/IGVFFI4045SHGK.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF1-BinB-PCR3-Rep1_S284.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2535ZPBT/",
"accession": "IGVFFI2535ZPBT",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR4-Rep1_S290"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:30:37.235850+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI2535ZPBT/@@download/IGVFFI2535ZPBT.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/8986029e-5350-4d78-9a14-df02923f1b0a/IGVFFI2535ZPBT.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF1-BinB-PCR4-Rep1_S290.yaml",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS1569RNPD/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS5572SQRK/",
"accession": "IGVFDS5572SQRK",
"aliases": [
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR1-Rep1_S242",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR2-Rep1_S248",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR3-Rep1_S284",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR4-Rep1_S290"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:09:18.397265+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5255ABUW/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5255ABUW",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR1-Rep1_S242",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR2-Rep1_S248",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR3-Rep1_S284",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR4-Rep1_S290"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS6351FGNG/"
],
"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 CCND1) treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours, modified with AID system targeting RAD21, CRISPRi Sp-dCas9-KOX1-KRAB, transfected 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": "2024-06-01T01:42:03.750959+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "265dbac8-d5f4-4d3c-b834-bca5102e6ec0"
}