{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS3648BJZO/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS3648BJZO",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF1-BinF-PCR1_S54",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF1-BinF-PCR2_S60",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF1-BinF-PCR3_S150",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF1-BinF-PCR4_S156"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS3648BJZO](/auxiliary-sets/IGVFDS3648BJZO/) has sequence file(s) [IGVFFI5733FMCC](/sequence-files/IGVFFI5733FMCC/), [IGVFFI4129KPOP](/sequence-files/IGVFFI4129KPOP/), [IGVFFI8751HVMX](/sequence-files/IGVFFI8751HVMX/), [IGVFFI9148EIXX](/sequence-files/IGVFFI9148EIXX/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS3648BJZO/"
}
]
},
"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": "2024-05-16T17:58:59.982191+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/IGVFFI5733FMCC/",
"accession": "IGVFFI5733FMCC",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF1-BinF-PCR1_S54"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:20:13.592648+00:00",
"file_format": "fastq",
"file_size": 10507677,
"href": "/sequence-files/IGVFFI5733FMCC/@@download/IGVFFI5733FMCC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/1449c486-66f4-49f6-a543-56707e40164f/IGVFFI5733FMCC.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF1-BinF-PCR1_S54_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2952DIBQ/",
"accession": "IGVFFI2952DIBQ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF1-BinF-PCR1_S54"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:09:31.380924+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI2952DIBQ/@@download/IGVFFI2952DIBQ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/d9ecda52-6f38-419e-afef-4f0a802f3d18/IGVFFI2952DIBQ.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF1-BinF-PCR1_S54.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4129KPOP/",
"accession": "IGVFFI4129KPOP",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF1-BinF-PCR4_S156"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T15:22:22.696192+00:00",
"file_format": "fastq",
"file_size": 22814962,
"href": "/sequence-files/IGVFFI4129KPOP/@@download/IGVFFI4129KPOP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/dad8db21-d399-46d9-855b-c9f3fdf03694/IGVFFI4129KPOP.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF1-BinF-PCR4_S156_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8751HVMX/",
"accession": "IGVFFI8751HVMX",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF1-BinF-PCR2_S60"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:20:34.304118+00:00",
"file_format": "fastq",
"file_size": 11547437,
"href": "/sequence-files/IGVFFI8751HVMX/@@download/IGVFFI8751HVMX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/b7880c9d-3322-4ab4-a62f-854a3af5366b/IGVFFI8751HVMX.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF1-BinF-PCR2_S60_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9148EIXX/",
"accession": "IGVFFI9148EIXX",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF1-BinF-PCR3_S150"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:20:52.525010+00:00",
"file_format": "fastq",
"file_size": 13010088,
"href": "/sequence-files/IGVFFI9148EIXX/@@download/IGVFFI9148EIXX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/af7561de-343a-478a-bc08-d6952802c1d5/IGVFFI9148EIXX.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF1-BinF-PCR3_S150_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6746VTYP/",
"accession": "IGVFFI6746VTYP",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF1-BinF-PCR3_S150"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:10:01.247965+00:00",
"file_format": "yaml",
"file_size": 904,
"href": "/configuration-files/IGVFFI6746VTYP/@@download/IGVFFI6746VTYP.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/5b4007bf-7f38-4476-bcdc-51e8ad5bbaf8/IGVFFI6746VTYP.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF1-BinF-PCR3_S150.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2400XTXC/",
"accession": "IGVFFI2400XTXC",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF1-BinF-PCR2_S60"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:09:46.376210+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI2400XTXC/@@download/IGVFFI2400XTXC.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/9ac52603-1edb-4d80-b189-47535becb633/IGVFFI2400XTXC.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF1-BinF-PCR2_S60.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0390EAUV/",
"accession": "IGVFFI0390EAUV",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF1-BinF-PCR4_S156"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:10:15.807953+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI0390EAUV/@@download/IGVFFI0390EAUV.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/007bdab5-98da-4e4f-8609-1d014b8dbabb/IGVFFI0390EAUV.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF1-BinF-PCR4_S156.yaml",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS6482AXWW/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS3973YRTN/",
"accession": "IGVFDS3973YRTN",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF1-BinF-PCR1_S54",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF1-BinF-PCR2_S60",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF1-BinF-PCR3_S150",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF1-BinF-PCR4_S156"
],
"preferred_assay_title": "CRISPR FlowFISH screen",
"status": "released"
}
],
"release_timestamp": "2024-07-10T20:16:56.610007+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9497VXWG/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9497VXWG",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF1-BinF-PCR1_S54",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF1-BinF-PCR2_S60",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF1-BinF-PCR3_S150",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF1-BinF-PCR4_S156"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS7846UISG/"
],
"modifications": [
{
"@id": "/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/",
"modality": "degradation",
"status": "released"
},
{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
"modality": "interference",
"status": "released"
}
],
"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 KITLG) 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": [
{
"@id": "/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/",
"status": "released",
"treatment_term_name": "5-Phenyl-1H-indole-3-acetic acid"
}
]
}
],
"schema_version": "12",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-01T02:20:13.592648+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "3847db20-6b69-441c-b51c-d80597297ead"
}