{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS2912UBNW/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS2912UBNW",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin6hrs-FF2-BinB-PCR1-Rep1_S38",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin6hrs-FF2-BinB-PCR2-Rep1_S44",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin6hrs-FF2-BinB-PCR3-Rep1_S92",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin6hrs-FF2-BinB-PCR4-Rep1_S98"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS2912UBNW](/auxiliary-sets/IGVFDS2912UBNW/) has sequence file(s) [IGVFFI9153DWPQ](/sequence-files/IGVFFI9153DWPQ/), [IGVFFI5807IMIA](/sequence-files/IGVFFI5807IMIA/), [IGVFFI2336DWVK](/sequence-files/IGVFFI2336DWVK/), [IGVFFI1581GQAT](/sequence-files/IGVFFI1581GQAT/) 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/IGVFDS2912UBNW/"
}
]
},
"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": "2024-05-14T21:06:43.793984+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/IGVFFI9153DWPQ/",
"accession": "IGVFFI9153DWPQ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF2-BinB-PCR1-Rep1_S38"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:48:21.266145+00:00",
"file_format": "fastq",
"file_size": 10927388,
"href": "/sequence-files/IGVFFI9153DWPQ/@@download/IGVFFI9153DWPQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/adafc80d-97b3-435b-9617-d241266ad520/IGVFFI9153DWPQ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin6hrs-FF2-BinB-PCR1-Rep1_S38_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4808EUZE/",
"accession": "IGVFFI4808EUZE",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF2-BinB-PCR1-Rep1_S38"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:40:47.898658+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI4808EUZE/@@download/IGVFFI4808EUZE.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/6d5398da-64c4-4792-a072-6e62d29081a6/IGVFFI4808EUZE.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF2-BinB-PCR1-Rep1_S38.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5807IMIA/",
"accession": "IGVFFI5807IMIA",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF2-BinB-PCR3-Rep1_S92"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:48:56.172068+00:00",
"file_format": "fastq",
"file_size": 23111315,
"href": "/sequence-files/IGVFFI5807IMIA/@@download/IGVFFI5807IMIA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/3e72ae5f-f027-4012-9668-88227e4f2b79/IGVFFI5807IMIA.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin6hrs-FF2-BinB-PCR3-Rep1_S92_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2336DWVK/",
"accession": "IGVFFI2336DWVK",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF2-BinB-PCR4-Rep1_S98"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:49:14.426429+00:00",
"file_format": "fastq",
"file_size": 16409162,
"href": "/sequence-files/IGVFFI2336DWVK/@@download/IGVFFI2336DWVK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/d7448e70-f528-48e9-9f09-6c26a952a0a0/IGVFFI2336DWVK.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin6hrs-FF2-BinB-PCR4-Rep1_S98_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0522BZGL/",
"accession": "IGVFFI0522BZGL",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF2-BinB-PCR2-Rep1_S44"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:41:04.029983+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI0522BZGL/@@download/IGVFFI0522BZGL.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/4dbb0f58-2abc-45dd-b1e9-9b04e693677a/IGVFFI0522BZGL.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF2-BinB-PCR2-Rep1_S44.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1581GQAT/",
"accession": "IGVFFI1581GQAT",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF2-BinB-PCR2-Rep1_S44"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:48:39.369803+00:00",
"file_format": "fastq",
"file_size": 16421333,
"href": "/sequence-files/IGVFFI1581GQAT/@@download/IGVFFI1581GQAT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/69b968da-e89f-4997-a657-be88ffac3a2c/IGVFFI1581GQAT.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin6hrs-FF2-BinB-PCR2-Rep1_S44_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4681CIZZ/",
"accession": "IGVFFI4681CIZZ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF2-BinB-PCR4-Rep1_S98"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:41:34.664672+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI4681CIZZ/@@download/IGVFFI4681CIZZ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/0e2a8a80-4d07-4b4f-8309-e7450e0190af/IGVFFI4681CIZZ.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF2-BinB-PCR4-Rep1_S98.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5154BJPK/",
"accession": "IGVFFI5154BJPK",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF2-BinB-PCR3-Rep1_S92"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:41:19.419791+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI5154BJPK/@@download/IGVFFI5154BJPK.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/1fc24344-bdbf-46e3-a26a-4c233195a3b0/IGVFFI5154BJPK.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF2-BinB-PCR3-Rep1_S92.yaml",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS2031CTSP/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS4798YRBK/",
"accession": "IGVFDS4798YRBK",
"aliases": [
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF2-BinB-PCR1-Rep1_S38",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF2-BinB-PCR2-Rep1_S44",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF2-BinB-PCR3-Rep1_S92",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF2-BinB-PCR4-Rep1_S98"
],
"preferred_assay_title": "CRISPR FlowFISH screen",
"status": "released"
}
],
"release_timestamp": "2024-07-10T20:25:58.907025+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0427NNRS/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0427NNRS",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF2-BinB-PCR1-Rep1_S38",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF2-BinB-PCR2-Rep1_S44",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF2-BinB-PCR3-Rep1_S92",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF2-BinB-PCR4-Rep1_S98"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS5413RKIA/"
],
"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 B for 10-20% expression of SSFA2) 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": "2024-06-01T01:48:21.266145+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "99f50ab6-c265-448d-b9fa-9be9668b4940"
}