{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS3113JRZB/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS3113JRZB",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF2-BinF-PCR1-Rep1_S234",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF2-BinF-PCR2-Rep1_S240",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF2-BinF-PCR3-Rep1_S276",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF2-BinF-PCR4-Rep1_S282"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS3113JRZB](/auxiliary-sets/IGVFDS3113JRZB/) has sequence file(s) [IGVFFI1527KBMM](/sequence-files/IGVFFI1527KBMM/), [IGVFFI6341VLOX](/sequence-files/IGVFFI6341VLOX/), [IGVFFI8605JNIH](/sequence-files/IGVFFI8605JNIH/), [IGVFFI4834NWWI](/sequence-files/IGVFFI4834NWWI/) 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/IGVFDS3113JRZB/"
}
]
},
"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": "2024-05-13T22:39:17.785760+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": [
{
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"accession": "IGVFFI1527KBMM",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF2-BinF-PCR1-Rep1_S234"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:37:23.666424+00:00",
"file_format": "fastq",
"file_size": 21373894,
"href": "/sequence-files/IGVFFI1527KBMM/@@download/IGVFFI1527KBMM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/9515480c-1515-4aff-93a3-2721321a3c49/IGVFFI1527KBMM.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/CCND1-Auxin0hrs-FF2-BinF-PCR1-Rep1_S234_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3189FDDL/",
"accession": "IGVFFI3189FDDL",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF2-BinF-PCR1-Rep1_S234"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:29:08.109676+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI3189FDDL/@@download/IGVFFI3189FDDL.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/3193ac8b-22e0-4a10-acbd-f1770abc4876/IGVFFI3189FDDL.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF2-BinF-PCR1-Rep1_S234.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6341VLOX/",
"accession": "IGVFFI6341VLOX",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF2-BinF-PCR2-Rep1_S240"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:37:41.157168+00:00",
"file_format": "fastq",
"file_size": 27921382,
"href": "/sequence-files/IGVFFI6341VLOX/@@download/IGVFFI6341VLOX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/4e5ed152-ebdb-4c08-a375-c0bf2a81493e/IGVFFI6341VLOX.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/CCND1-Auxin0hrs-FF2-BinF-PCR2-Rep1_S240_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8605JNIH/",
"accession": "IGVFFI8605JNIH",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF2-BinF-PCR3-Rep1_S276"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:37:59.600072+00:00",
"file_format": "fastq",
"file_size": 23844775,
"href": "/sequence-files/IGVFFI8605JNIH/@@download/IGVFFI8605JNIH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/3fb7c215-9cb0-47ff-b9b1-2597552a405c/IGVFFI8605JNIH.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/CCND1-Auxin0hrs-FF2-BinF-PCR3-Rep1_S276_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4834NWWI/",
"accession": "IGVFFI4834NWWI",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF2-BinF-PCR4-Rep1_S282"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:41:57.154698+00:00",
"file_format": "fastq",
"file_size": 38906030,
"href": "/sequence-files/IGVFFI4834NWWI/@@download/IGVFFI4834NWWI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/d8f56d88-ee0e-4fb1-ac66-d6017ea36970/IGVFFI4834NWWI.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/CCND1-Auxin0hrs-FF2-BinF-PCR4-Rep1_S282_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7128IGSG/",
"accession": "IGVFFI7128IGSG",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF2-BinF-PCR4-Rep1_S282"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:29:49.890588+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI7128IGSG/@@download/IGVFFI7128IGSG.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/8aa436e8-d858-422c-858e-6a235a0a1754/IGVFFI7128IGSG.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF2-BinF-PCR4-Rep1_S282.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9477RRHF/",
"accession": "IGVFFI9477RRHF",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF2-BinF-PCR2-Rep1_S240"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:29:21.932790+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI9477RRHF/@@download/IGVFFI9477RRHF.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/2f1dbb0f-0038-4fab-9b42-c3e87f178a27/IGVFFI9477RRHF.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF2-BinF-PCR2-Rep1_S240.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0638MCOK/",
"accession": "IGVFFI0638MCOK",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF2-BinF-PCR3-Rep1_S276"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:29:35.882180+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI0638MCOK/@@download/IGVFFI0638MCOK.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/e1dc87f7-7871-4d51-ad83-3c9a5f1ca104/IGVFFI0638MCOK.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF2-BinF-PCR3-Rep1_S276.yaml",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS1569RNPD/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS3504GXZA/",
"accession": "IGVFDS3504GXZA",
"aliases": [
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF2-BinF-PCR1-Rep1_S234",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF2-BinF-PCR2-Rep1_S240",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF2-BinF-PCR3-Rep1_S276",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF2-BinF-PCR4-Rep1_S282"
],
"preferred_assay_title": "CRISPR FlowFISH screen",
"status": "released"
}
],
"release_timestamp": "2024-07-10T20:09:04.736045+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM6932DXSV/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6932DXSV",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF2-BinF-PCR1-Rep1_S234",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF2-BinF-PCR2-Rep1_S240",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF2-BinF-PCR3-Rep1_S276",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF2-BinF-PCR4-Rep1_S282"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS6351FGNG/"
],
"modifications": [
{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
"modality": "interference",
"status": "released"
},
{
"@id": "/degron-modifications/2e8d10cc-fc98-44d5-a7d9-e2892e16c98a/",
"modality": "degradation",
"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 CCND1) modified with CRISPRi Sp-dCas9-KOX1-KRAB, inactive AID system targeting RAD21, transfected with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "12",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-01T01:37:23.666424+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "4c926831-d816-4cff-9465-5c3e6a9fbe01"
}