{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS8871HVZU/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS8871HVZU",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF1-BinA-PCR1-Rep1_S109",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF1-BinA-PCR2-Rep1_S115",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF1-BinA-PCR3-Rep1_S163",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF1-BinA-PCR4-Rep1_S169"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS8871HVZU](/auxiliary-sets/IGVFDS8871HVZU/) has sequence file(s) [IGVFFI4047DOQR](/sequence-files/IGVFFI4047DOQR/), [IGVFFI5610GEDM](/sequence-files/IGVFFI5610GEDM/), [IGVFFI8800QUFB](/sequence-files/IGVFFI8800QUFB/), [IGVFFI3269HFXQ](/sequence-files/IGVFFI3269HFXQ/) 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/IGVFDS8871HVZU/"
}
]
},
"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": "2024-05-14T16:23:49.600771+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": "IGVFFI4047DOQR",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:50:49.609086+00:00",
"file_format": "fastq",
"file_size": 33957548,
"href": "/sequence-files/IGVFFI4047DOQR/@@download/IGVFFI4047DOQR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/bb35b7fb-9499-4639-8753-cd3f35af1a33/IGVFFI4047DOQR.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/FAM3C-Auxin0hrs-FF1-BinA-PCR1-Rep1_S109_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7993DQGZ/",
"accession": "IGVFFI7993DQGZ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF1-BinA-PCR1-Rep1_S109"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:41:49.365610+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI7993DQGZ/@@download/IGVFFI7993DQGZ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/8bc82b03-ad8a-4ff2-8d93-91aedc556a4e/IGVFFI7993DQGZ.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF1-BinA-PCR1-Rep1_S109.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5610GEDM/",
"accession": "IGVFFI5610GEDM",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF1-BinA-PCR2-Rep1_S115"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:51:10.148422+00:00",
"file_format": "fastq",
"file_size": 24342273,
"href": "/sequence-files/IGVFFI5610GEDM/@@download/IGVFFI5610GEDM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/bd623ad6-8f1f-452f-87b9-a6793c76e1bf/IGVFFI5610GEDM.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/FAM3C-Auxin0hrs-FF1-BinA-PCR2-Rep1_S115_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8800QUFB/",
"accession": "IGVFFI8800QUFB",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF1-BinA-PCR3-Rep1_S163"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:51:28.642686+00:00",
"file_format": "fastq",
"file_size": 32923471,
"href": "/sequence-files/IGVFFI8800QUFB/@@download/IGVFFI8800QUFB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/56b3e603-2e3d-4076-84ad-9797ffd0b5e7/IGVFFI8800QUFB.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/FAM3C-Auxin0hrs-FF1-BinA-PCR3-Rep1_S163_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3269HFXQ/",
"accession": "IGVFFI3269HFXQ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF1-BinA-PCR4-Rep1_S169"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:51:47.738838+00:00",
"file_format": "fastq",
"file_size": 29829564,
"href": "/sequence-files/IGVFFI3269HFXQ/@@download/IGVFFI3269HFXQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/82ad45b8-4345-4f90-9fcb-2b774f6f5abc/IGVFFI3269HFXQ.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/FAM3C-Auxin0hrs-FF1-BinA-PCR4-Rep1_S169_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0611SUFM/",
"accession": "IGVFFI0611SUFM",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF1-BinA-PCR4-Rep1_S169"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:42:33.082332+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI0611SUFM/@@download/IGVFFI0611SUFM.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/8466861c-db64-4520-b916-70c93b67b543/IGVFFI0611SUFM.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF1-BinA-PCR4-Rep1_S169.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7093PHJH/",
"accession": "IGVFFI7093PHJH",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF1-BinA-PCR2-Rep1_S115"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:42:05.036938+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI7093PHJH/@@download/IGVFFI7093PHJH.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/a6041667-4d7c-4cc2-ad98-dd9911432087/IGVFFI7093PHJH.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF1-BinA-PCR2-Rep1_S115.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0987YOBQ/",
"accession": "IGVFFI0987YOBQ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF1-BinA-PCR3-Rep1_S163"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:42:19.953519+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI0987YOBQ/@@download/IGVFFI0987YOBQ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/3dcc9ff0-f038-409d-b30d-6b1a3030e8d4/IGVFFI0987YOBQ.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF1-BinA-PCR3-Rep1_S163.yaml",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS5239VQTN/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS6095WNVW/",
"accession": "IGVFDS6095WNVW",
"aliases": [
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF1-BinA-PCR1-Rep1_S109",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF1-BinA-PCR2-Rep1_S115",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF1-BinA-PCR3-Rep1_S163",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF1-BinA-PCR4-Rep1_S169"
],
"preferred_assay_title": "CRISPR FlowFISH screen",
"status": "released"
}
],
"release_timestamp": "2024-07-10T20:10:38.272539+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5410WZKF/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5410WZKF",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF1-BinA-PCR1-Rep1_S109",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF1-BinA-PCR2-Rep1_S115",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF1-BinA-PCR3-Rep1_S163",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF1-BinA-PCR4-Rep1_S169"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS1891GTLU/"
],
"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 A for 0-10% expression of FAM3C) 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": "2024-06-01T01:50:49.609086+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "e895b5f3-32d2-4196-a1d8-b75cbedf24e1"
}