{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS3611WVHW/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS3611WVHW",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF1-BinE-PCR1-Rep1_S113",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF1-BinE-PCR2-Rep1_S119",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF1-BinE-PCR3-Rep1_S167",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF1-BinE-PCR4-Rep1_S173"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS3611WVHW](/auxiliary-sets/IGVFDS3611WVHW/) has sequence file(s) [IGVFFI8497NPVR](/sequence-files/IGVFFI8497NPVR/), [IGVFFI0840FMQW](/sequence-files/IGVFFI0840FMQW/), [IGVFFI7555FXHU](/sequence-files/IGVFFI7555FXHU/), [IGVFFI0393VYGB](/sequence-files/IGVFFI0393VYGB/) 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/IGVFDS3611WVHW/"
}
]
},
"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": "2024-05-14T16:23:54.784069+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/IGVFFI8497NPVR/",
"accession": "IGVFFI8497NPVR",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF1-BinE-PCR1-Rep1_S113"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:51:03.804629+00:00",
"file_format": "fastq",
"file_size": 18858257,
"href": "/sequence-files/IGVFFI8497NPVR/@@download/IGVFFI8497NPVR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/2e730e47-783c-41a9-bcac-943971d7eb30/IGVFFI8497NPVR.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-BinE-PCR1-Rep1_S113_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1875AKLE/",
"accession": "IGVFFI1875AKLE",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF1-BinE-PCR1-Rep1_S113"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:41:59.862244+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI1875AKLE/@@download/IGVFFI1875AKLE.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/acee7f90-56b8-4d88-9996-42d85077752e/IGVFFI1875AKLE.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF1-BinE-PCR1-Rep1_S113.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0840FMQW/",
"accession": "IGVFFI0840FMQW",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF1-BinE-PCR2-Rep1_S119"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:51:22.667705+00:00",
"file_format": "fastq",
"file_size": 24853329,
"href": "/sequence-files/IGVFFI0840FMQW/@@download/IGVFFI0840FMQW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/f43ab3e5-3f39-4f91-866d-03c4f3f0cd44/IGVFFI0840FMQW.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-BinE-PCR2-Rep1_S119_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7555FXHU/",
"accession": "IGVFFI7555FXHU",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF1-BinE-PCR3-Rep1_S167"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:51:40.927275+00:00",
"file_format": "fastq",
"file_size": 24620913,
"href": "/sequence-files/IGVFFI7555FXHU/@@download/IGVFFI7555FXHU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/9a1dc410-cde1-4b78-95c5-464e29c0c356/IGVFFI7555FXHU.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-BinE-PCR3-Rep1_S167_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0393VYGB/",
"accession": "IGVFFI0393VYGB",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF1-BinE-PCR4-Rep1_S173"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:52:00.458588+00:00",
"file_format": "fastq",
"file_size": 29643478,
"href": "/sequence-files/IGVFFI0393VYGB/@@download/IGVFFI0393VYGB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/fae35da2-9903-466a-9445-de0b7393cb4e/IGVFFI0393VYGB.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-BinE-PCR4-Rep1_S173_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0081OFZM/",
"accession": "IGVFFI0081OFZM",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF1-BinE-PCR2-Rep1_S119"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:42:15.178823+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI0081OFZM/@@download/IGVFFI0081OFZM.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/8b3d9272-eb90-4386-953e-92b6a1f3cff7/IGVFFI0081OFZM.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF1-BinE-PCR2-Rep1_S119.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1460IMUJ/",
"accession": "IGVFFI1460IMUJ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF1-BinE-PCR4-Rep1_S173"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:42:41.944823+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI1460IMUJ/@@download/IGVFFI1460IMUJ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/48546bdb-1b17-4308-87e7-384983cd1054/IGVFFI1460IMUJ.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF1-BinE-PCR4-Rep1_S173.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9021TJZW/",
"accession": "IGVFFI9021TJZW",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF1-BinE-PCR3-Rep1_S167"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:42:28.524961+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI9021TJZW/@@download/IGVFFI9021TJZW.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/27360650-8282-4829-862c-7723a93b0989/IGVFFI9021TJZW.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF1-BinE-PCR3-Rep1_S167.yaml",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS5239VQTN/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS5612XEIT/",
"accession": "IGVFDS5612XEIT",
"aliases": [
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF1-BinE-PCR1-Rep1_S113",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF1-BinE-PCR2-Rep1_S119",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF1-BinE-PCR3-Rep1_S167",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF1-BinE-PCR4-Rep1_S173"
],
"preferred_assay_title": "CRISPR FlowFISH screen",
"status": "released"
}
],
"release_timestamp": "2024-07-10T20:11:07.720466+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4222TCYN/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4222TCYN",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF1-BinE-PCR1-Rep1_S113",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF1-BinE-PCR2-Rep1_S119",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF1-BinE-PCR3-Rep1_S167",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF1-BinE-PCR4-Rep1_S173"
],
"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 E for 80-90% 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": "2024-06-01T01:51:03.804629+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "79faf7d1-2e28-4f7c-a9c2-cafd0e17779a"
}