{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS7242NZGL/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS7242NZGL",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinC-PCR1_S75",
"jesse-engreitz:auxiliary_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinC-PCR2_S171",
"jesse-engreitz:auxiliary_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinC-PCR3_S267",
"jesse-engreitz:auxiliary_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinC-PCR4_S363"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS7242NZGL](/auxiliary-sets/IGVFDS7242NZGL/) has sequence file(s) [IGVFFI2478ZHXM](/sequence-files/IGVFFI2478ZHXM/), [IGVFFI3891DAKN](/sequence-files/IGVFFI3891DAKN/), [IGVFFI1779JDBV](/sequence-files/IGVFFI1779JDBV/), [IGVFFI3057BHFY](/sequence-files/IGVFFI3057BHFY/) 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/IGVFDS7242NZGL/"
}
]
},
"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": "2024-05-06T23:13:49.885492+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": "IGVFFI2478ZHXM",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinC-PCR1_S75"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:29:17.578944+00:00",
"file_format": "fastq",
"file_size": 3094136,
"href": "/sequence-files/IGVFFI2478ZHXM/@@download/IGVFFI2478ZHXM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/6d5d4317-a2b6-43fe-b3f9-93f5d839303a/IGVFFI2478ZHXM.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/210301B002-CohesinFF/fastq/CCND1-Auxin0hrs-FF1-BinC-PCR1_S75_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2303ZRST/",
"accession": "IGVFFI2303ZRST",
"aliases": [
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],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:23:52.731950+00:00",
"file_format": "yaml",
"file_size": 910,
"href": "/configuration-files/IGVFFI2303ZRST/@@download/IGVFFI2303ZRST.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/c20379ac-6308-4ca0-b524-67c0978f5883/IGVFFI2303ZRST.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin0hrs-FF1-BinC-PCR1_S75.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7524EEOV/",
"accession": "IGVFFI7524EEOV",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinC-PCR4_S363"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:24:32.368108+00:00",
"file_format": "yaml",
"file_size": 910,
"href": "/configuration-files/IGVFFI7524EEOV/@@download/IGVFFI7524EEOV.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/c977f16f-498d-4d6b-b0af-a5acf2cf55cc/IGVFFI7524EEOV.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin0hrs-FF1-BinC-PCR4_S363.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3891DAKN/",
"accession": "IGVFFI3891DAKN",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinC-PCR2_S171"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:29:33.319591+00:00",
"file_format": "fastq",
"file_size": 6894019,
"href": "/sequence-files/IGVFFI3891DAKN/@@download/IGVFFI3891DAKN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/654217a7-abdd-4a1e-bbd7-07dd9ede9499/IGVFFI3891DAKN.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/210301B002-CohesinFF/fastq/CCND1-Auxin0hrs-FF1-BinC-PCR2_S171_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1779JDBV/",
"accession": "IGVFFI1779JDBV",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinC-PCR3_S267"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:29:49.664817+00:00",
"file_format": "fastq",
"file_size": 6228237,
"href": "/sequence-files/IGVFFI1779JDBV/@@download/IGVFFI1779JDBV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/1c5816f5-fbb8-49e1-90be-a90bd5780a41/IGVFFI1779JDBV.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/210301B002-CohesinFF/fastq/CCND1-Auxin0hrs-FF1-BinC-PCR3_S267_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3057BHFY/",
"accession": "IGVFFI3057BHFY",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinC-PCR4_S363"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:30:06.111033+00:00",
"file_format": "fastq",
"file_size": 6268071,
"href": "/sequence-files/IGVFFI3057BHFY/@@download/IGVFFI3057BHFY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/8606e457-c3b5-419b-9fec-73fd395b58c9/IGVFFI3057BHFY.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/210301B002-CohesinFF/fastq/CCND1-Auxin0hrs-FF1-BinC-PCR4_S363_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2438PQQQ/",
"accession": "IGVFFI2438PQQQ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinC-PCR3_S267"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:24:19.112107+00:00",
"file_format": "yaml",
"file_size": 909,
"href": "/configuration-files/IGVFFI2438PQQQ/@@download/IGVFFI2438PQQQ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/9375b6a2-9400-46e8-8f71-37917a155c61/IGVFFI2438PQQQ.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin0hrs-FF1-BinC-PCR3_S267.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4790WUCA/",
"accession": "IGVFFI4790WUCA",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinC-PCR2_S171"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:24:05.847995+00:00",
"file_format": "yaml",
"file_size": 908,
"href": "/configuration-files/IGVFFI4790WUCA/@@download/IGVFFI4790WUCA.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/47cf084d-f5cf-4caa-b1b8-ec41a2d82ebf/IGVFFI4790WUCA.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin0hrs-FF1-BinC-PCR2_S171.yaml",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS2982SJGW/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS2046SNMC/",
"accession": "IGVFDS2046SNMC",
"aliases": [
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinC-PCR1_S75",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinC-PCR2_S171",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinC-PCR3_S267",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinC-PCR4_S363"
],
"preferred_assay_title": "CRISPR FlowFISH screen",
"status": "released"
}
],
"release_timestamp": "2024-07-10T20:22:31.539442+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5079ZTJX/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5079ZTJX",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinC-PCR1_S75",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinC-PCR2_S171",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinC-PCR3_S267",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinC-PCR4_S363"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS0392OWNZ/"
],
"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 C for 35-45% 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": "2024-06-01T01:29:17.578944+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in 36 genomic loci",
"uuid": "d8084496-2096-47e2-9cb5-71b6f25361cf"
}