{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS4450DYPE/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS4450DYPE",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF2-BinC-PCR1-Rep1_S123",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF2-BinC-PCR2-Rep1_S129",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF2-BinC-PCR3-Rep1_S177",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF2-BinC-PCR4-Rep1_S183"
],
"audit": {
"NOT_COMPLIANT": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS4450DYPE](/auxiliary-sets/IGVFDS4450DYPE/) has sequence file(s) [IGVFFI9121LPRU](/sequence-files/IGVFFI9121LPRU/), [IGVFFI0549HJLD](/sequence-files/IGVFFI0549HJLD/), [IGVFFI2535IDQZ](/sequence-files/IGVFFI2535IDQZ/), [IGVFFI1717GCIU](/sequence-files/IGVFFI1717GCIU/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS4450DYPE/"
}
]
},
"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": "2024-05-14T16:24:20.814724+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/IGVFFI9121LPRU/",
"accession": "IGVFFI9121LPRU",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF2-BinC-PCR1-Rep1_S123"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:52:12.776673+00:00",
"file_format": "fastq",
"file_size": 21593401,
"href": "/sequence-files/IGVFFI9121LPRU/@@download/IGVFFI9121LPRU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/5aaf2aa7-eaef-4a23-8140-1956c8ec2b7c/IGVFFI9121LPRU.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/FAM3C-Auxin0hrs-FF2-BinC-PCR1-Rep1_S123_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8791TABE/",
"accession": "IGVFFI8791TABE",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF2-BinC-PCR1-Rep1_S123"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:42:51.025981+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI8791TABE/@@download/IGVFFI8791TABE.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/3ce25733-e31f-46e9-8d71-74f79da141b6/IGVFFI8791TABE.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF2-BinC-PCR1-Rep1_S123.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0549HJLD/",
"accession": "IGVFFI0549HJLD",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF2-BinC-PCR2-Rep1_S129"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:52:31.176927+00:00",
"file_format": "fastq",
"file_size": 25001688,
"href": "/sequence-files/IGVFFI0549HJLD/@@download/IGVFFI0549HJLD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/e2d70b6c-44cc-47cc-a330-37a9b8a5841b/IGVFFI0549HJLD.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/FAM3C-Auxin0hrs-FF2-BinC-PCR2-Rep1_S129_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2535IDQZ/",
"accession": "IGVFFI2535IDQZ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF2-BinC-PCR3-Rep1_S177"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:52:49.269972+00:00",
"file_format": "fastq",
"file_size": 27700691,
"href": "/sequence-files/IGVFFI2535IDQZ/@@download/IGVFFI2535IDQZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/ba4930f5-90c6-4c4e-8a74-9af081182d19/IGVFFI2535IDQZ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/FAM3C-Auxin0hrs-FF2-BinC-PCR3-Rep1_S177_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1717GCIU/",
"accession": "IGVFFI1717GCIU",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF2-BinC-PCR4-Rep1_S183"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:53:07.420729+00:00",
"file_format": "fastq",
"file_size": 32920168,
"href": "/sequence-files/IGVFFI1717GCIU/@@download/IGVFFI1717GCIU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/b8e2b3c8-93fe-473b-a46f-c1a4c651db2c/IGVFFI1717GCIU.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/FAM3C-Auxin0hrs-FF2-BinC-PCR4-Rep1_S183_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4325KHUA/",
"accession": "IGVFFI4325KHUA",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF2-BinC-PCR4-Rep1_S183"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:43:32.133482+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI4325KHUA/@@download/IGVFFI4325KHUA.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/ff48bb38-f790-4271-ab93-e2ea8fb2f8c1/IGVFFI4325KHUA.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF2-BinC-PCR4-Rep1_S183.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8762RUFJ/",
"accession": "IGVFFI8762RUFJ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF2-BinC-PCR3-Rep1_S177"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:43:18.845388+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI8762RUFJ/@@download/IGVFFI8762RUFJ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/cfff8397-afb7-48e3-9b9b-a95872ba8dd9/IGVFFI8762RUFJ.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF2-BinC-PCR3-Rep1_S177.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6912NVOR/",
"accession": "IGVFFI6912NVOR",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF2-BinC-PCR2-Rep1_S129"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:43:04.714593+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI6912NVOR/@@download/IGVFFI6912NVOR.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/e3ac64c4-b7df-4117-900c-8246e5132b9d/IGVFFI6912NVOR.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF2-BinC-PCR2-Rep1_S129.yaml",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS5239VQTN/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS8728GREK/",
"accession": "IGVFDS8728GREK",
"aliases": [
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF2-BinC-PCR1-Rep1_S123",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF2-BinC-PCR2-Rep1_S129",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF2-BinC-PCR3-Rep1_S177",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF2-BinC-PCR4-Rep1_S183"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:11:35.822032+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0890WDDX/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0890WDDX",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF2-BinC-PCR1-Rep1_S123",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF2-BinC-PCR2-Rep1_S129",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF2-BinC-PCR3-Rep1_S177",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF2-BinC-PCR4-Rep1_S183"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS1891GTLU/"
],
"modifications": [
"/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
"/degron-modifications/2e8d10cc-fc98-44d5-a7d9-e2892e16c98a/"
],
"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 FAM3C) modified with CRISPRi Sp-dCas9-KOX1-KRAB, inactive AID system targeting RAD21, transfected with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "11",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-01T01:52:12.776673+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "187a77e0-feb5-4ddc-9b76-5c7a1c12fb48"
}