{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS3348ANJX/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS3348ANJX",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF1-BinB-PCR1-Rep1_S218",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF1-BinB-PCR2-Rep1_S224",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF1-BinB-PCR3-Rep1_S260",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF1-BinB-PCR4-Rep1_S266"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released human donor [IGVFDO0384OZRW](/human-donors/IGVFDO0384OZRW/) has in progress subobject publication [155f24ce-5c2c-4400-8651-da9447eaca25](/publications/155f24ce-5c2c-4400-8651-da9447eaca25/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO0384OZRW/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS3348ANJX](/auxiliary-sets/IGVFDS3348ANJX/) has sequence file(s) [IGVFFI2449YPRX](/sequence-files/IGVFFI2449YPRX/), [IGVFFI2197JQZH](/sequence-files/IGVFFI2197JQZH/), [IGVFFI7504AYGF](/sequence-files/IGVFFI7504AYGF/), [IGVFFI8736GAXG](/sequence-files/IGVFFI8736GAXG/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 40,
"level_name": "WARNING",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS3348ANJX/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS3348ANJX](/auxiliary-sets/IGVFDS3348ANJX/) is a raw data set with files, but is not listed in any `input_file_sets` for any analysis sets. Raw data sets with files are expected to be associated with at least one analysis set.",
"level": 40,
"level_name": "WARNING",
"name": "audit_input_file_set_for",
"path": "/auxiliary-sets/IGVFDS3348ANJX/"
}
]
},
"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": "2024-05-13T22:38:45.791598+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/IGVFFI2449YPRX/",
"accession": "IGVFFI2449YPRX",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF1-BinB-PCR1-Rep1_S218"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:35:58.828749+00:00",
"file_format": "fastq",
"file_size": 20357822,
"href": "/sequence-files/IGVFFI2449YPRX/@@download/IGVFFI2449YPRX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/9de2b80e-64c4-428a-bdb5-130477f71c22/IGVFFI2449YPRX.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin0hrs-FF1-BinB-PCR1-Rep1_S218_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3802OHJV/",
"accession": "IGVFFI3802OHJV",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF1-BinB-PCR1-Rep1_S218"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:28:00.604447+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI3802OHJV/@@download/IGVFFI3802OHJV.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/2d8a1c91-9013-4052-b5fc-e730fa5a4d8d/IGVFFI3802OHJV.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF1-BinB-PCR1-Rep1_S218.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2197JQZH/",
"accession": "IGVFFI2197JQZH",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF1-BinB-PCR2-Rep1_S224"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:36:17.163881+00:00",
"file_format": "fastq",
"file_size": 17414536,
"href": "/sequence-files/IGVFFI2197JQZH/@@download/IGVFFI2197JQZH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/5a032432-f156-4357-b339-e413d4e803a2/IGVFFI2197JQZH.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin0hrs-FF1-BinB-PCR2-Rep1_S224_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7504AYGF/",
"accession": "IGVFFI7504AYGF",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF1-BinB-PCR3-Rep1_S260"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:36:35.505269+00:00",
"file_format": "fastq",
"file_size": 29761536,
"href": "/sequence-files/IGVFFI7504AYGF/@@download/IGVFFI7504AYGF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/8d7ac1d0-53db-460f-adb6-f3c20e4884f7/IGVFFI7504AYGF.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin0hrs-FF1-BinB-PCR3-Rep1_S260_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8736GAXG/",
"accession": "IGVFFI8736GAXG",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF1-BinB-PCR4-Rep1_S266"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:36:53.479366+00:00",
"file_format": "fastq",
"file_size": 22299303,
"href": "/sequence-files/IGVFFI8736GAXG/@@download/IGVFFI8736GAXG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/e13d33e2-459d-4083-ac8d-bf4889167ddf/IGVFFI8736GAXG.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin0hrs-FF1-BinB-PCR4-Rep1_S266_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3031TSMB/",
"accession": "IGVFFI3031TSMB",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF1-BinB-PCR4-Rep1_S266"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:28:43.733511+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI3031TSMB/@@download/IGVFFI3031TSMB.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/cd8ddf3b-5291-46cc-a010-0e0bc3316169/IGVFFI3031TSMB.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF1-BinB-PCR4-Rep1_S266.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2565KLMK/",
"accession": "IGVFFI2565KLMK",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF1-BinB-PCR2-Rep1_S224"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:28:15.580979+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI2565KLMK/@@download/IGVFFI2565KLMK.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/31a4cc72-fe92-4556-bac6-57b2a689348a/IGVFFI2565KLMK.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF1-BinB-PCR2-Rep1_S224.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9789NJOA/",
"accession": "IGVFFI9789NJOA",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF1-BinB-PCR3-Rep1_S260"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:28:29.716009+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI9789NJOA/@@download/IGVFFI9789NJOA.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/521ad941-963d-4208-8ab3-f42b6feace7b/IGVFFI9789NJOA.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF1-BinB-PCR3-Rep1_S260.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS7173YRIO/",
"accession": "IGVFDS7173YRIO",
"aliases": [
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinB-PCR1-Rep1_S218",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinB-PCR2-Rep1_S224",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinB-PCR3-Rep1_S260",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinB-PCR4-Rep1_S266"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:07:56.763494+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4779RXHT/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4779RXHT",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinB-PCR1-Rep1_S218",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinB-PCR2-Rep1_S224",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinB-PCR3-Rep1_S260",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinB-PCR4-Rep1_S266"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS6351FGNG/"
],
"modifications": [
"/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/"
],
"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 B for 10-20% expression of CCND1) modified 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": "2024-06-01T01:35:58.828749+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "f1136615-c3a2-4ca5-8697-b975c32abc30"
}