{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5387BSQH/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5387BSQH",
"aliases": [
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF2-BinF-PCR1-Rep1_S306",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF2-BinF-PCR2-Rep1_S312",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF2-BinF-PCR3-Rep1_S324",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF2-BinF-PCR4-Rep1_S330"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"assay_slims": [
"CRISPR screens"
],
"status": "released",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"ERROR": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS5387BSQH](/measurement-sets/IGVFDS5387BSQH/) links to sample [IGVFSM0402MSVI](/in-vitro-systems/IGVFSM0402MSVI/) which links to auxiliary set [IGVFDS1065WJDZ](/auxiliary-sets/IGVFDS1065WJDZ/) but is not in its `auxiliary_sets`. Measurement sets are expected to link to auxiliary sets if they share the same sample.",
"level": 60,
"level_name": "ERROR",
"name": "audit_missing_auxiliary_set_link",
"path": "/measurement-sets/IGVFDS5387BSQH/"
}
],
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM0402MSVI](/in-vitro-systems/IGVFSM0402MSVI/) has no `publications`. Released and archived samples are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_sample_missing_publication",
"path": "/in-vitro-systems/IGVFSM0402MSVI/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS5387BSQH](/measurement-sets/IGVFDS5387BSQH/) has no `publications`. Released and archived file sets are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_file_set_missing_publication",
"path": "/measurement-sets/IGVFDS5387BSQH/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS5387BSQH](/measurement-sets/IGVFDS5387BSQH/) has sequence file(s) [IGVFFI9698DUHO](/sequence-files/IGVFFI9698DUHO/), [IGVFFI4262NYMF](/sequence-files/IGVFFI4262NYMF/), [IGVFFI1935DBLW](/sequence-files/IGVFFI1935DBLW/), [IGVFFI8971PQCM](/sequence-files/IGVFFI8971PQCM/) which lack specification of a `sequencing_kit`. Sequence files in a file set associated wtih bulk data should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/measurement-sets/IGVFDS5387BSQH/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS5387BSQH](/measurement-sets/IGVFDS5387BSQH/) has revoked subobject auxiliary set [IGVFDS0720TXUF](/auxiliary-sets/IGVFDS0720TXUF/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS5387BSQH/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing files",
"detail": "Auxiliary set [IGVFDS0720TXUF](/auxiliary-sets/IGVFDS0720TXUF/) has no `files`. File sets are expected to have files.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_no_files",
"path": "/auxiliary-sets/IGVFDS0720TXUF/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM0402MSVI](/in-vitro-systems/IGVFSM0402MSVI/) has `construct_library_sets` but is missing `nucleic_acid_delivery`. Samples linked to construct library sets are expected to specify nucleic acid delivery method.",
"level": 40,
"level_name": "WARNING",
"name": "audit_missing_nucleic_acid_delivery",
"path": "/in-vitro-systems/IGVFSM0402MSVI/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS5387BSQH](/measurement-sets/IGVFDS5387BSQH/) has no cell sorting `auxiliary_sets`. CRISPR-based measurement sets that utilize flow cytometry are expected to link to a cell sorting auxiliary set.",
"level": 40,
"level_name": "WARNING",
"name": "audit_missing_auxiliary_set",
"path": "/measurement-sets/IGVFDS5387BSQH/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS0720TXUF/",
"accession": "IGVFDS0720TXUF",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF2-BinF-PCR1-Rep1_S306",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF2-BinF-PCR2-Rep1_S312",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF2-BinF-PCR3-Rep1_S324",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF2-BinF-PCR4-Rep1_S330"
],
"file_set_type": "gRNA sequencing",
"status": "revoked"
}
],
"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"
},
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS6351FGNG/",
"accession": "IGVFDS6351FGNG",
"file_set_type": "guide library",
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI5924HOIN/",
"accession": "IGVFFI5924HOIN",
"content_type": "guide RNA sequences",
"status": "released",
"summary": "guide RNA sequences"
}
],
"status": "released",
"summary": "guide (sgRNA) library targeting accessible genome regions in many genomic loci"
}
],
"control_for": [],
"creation_timestamp": "2024-05-13T22:16:59.537551+00:00",
"documents": [
"/documents/74d53b9c-ab1d-42e3-b679-d3a00ae3d842/"
],
"donors": [
{
"@id": "/human-donors/IGVFDO0384OZRW/",
"accession": "IGVFDO0384OZRW",
"aliases": [
"igvf:donor_of_HCT116"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/configuration-files/IGVFFI2184MRDQ/",
"accession": "IGVFFI2184MRDQ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF2-BinF-PCR2-Rep1_S312"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:31:14.396214+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI2184MRDQ/@@download/IGVFFI2184MRDQ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/b86deb38-986f-44c6-84f8-6d3705e8942c/IGVFFI2184MRDQ.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF2-BinF-PCR2-Rep1_S312.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI9698DUHO/",
"accession": "IGVFFI9698DUHO",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF2-BinF-PCR4-Rep1_S330"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:44:18.304916+00:00",
"file_format": "fastq",
"file_size": 25446426,
"href": "/sequence-files/IGVFFI9698DUHO/@@download/IGVFFI9698DUHO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/ca260c91-a986-46fe-b76b-0e2ddd064c1b/IGVFFI9698DUHO.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008565/",
"status": "released",
"term_name": "Illumina HiSeq 2500"
},
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin6hrs-FF2-BinF-PCR4-Rep1_S330_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4262NYMF/",
"accession": "IGVFFI4262NYMF",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF2-BinF-PCR1-Rep1_S306"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:43:26.766525+00:00",
"file_format": "fastq",
"file_size": 13369840,
"href": "/sequence-files/IGVFFI4262NYMF/@@download/IGVFFI4262NYMF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/f31ba84a-08c2-416c-927b-fe114cdcce4c/IGVFFI4262NYMF.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008565/",
"status": "released",
"term_name": "Illumina HiSeq 2500"
},
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin6hrs-FF2-BinF-PCR1-Rep1_S306_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5413XAFZ/",
"accession": "IGVFFI5413XAFZ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF2-BinF-PCR1-Rep1_S306"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:31:00.244067+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI5413XAFZ/@@download/IGVFFI5413XAFZ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/d6d122ad-3d65-44cf-ba19-2567e3084283/IGVFFI5413XAFZ.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF2-BinF-PCR1-Rep1_S306.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI7503ZAVZ/",
"accession": "IGVFFI7503ZAVZ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF2-BinF-PCR3-Rep1_S324"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:31:28.488829+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI7503ZAVZ/@@download/IGVFFI7503ZAVZ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/c5ab8c48-3ad4-4b23-9228-ae1a8a8774ff/IGVFFI7503ZAVZ.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF2-BinF-PCR3-Rep1_S324.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI1935DBLW/",
"accession": "IGVFFI1935DBLW",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF2-BinF-PCR2-Rep1_S312"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:43:43.848038+00:00",
"file_format": "fastq",
"file_size": 12237502,
"href": "/sequence-files/IGVFFI1935DBLW/@@download/IGVFFI1935DBLW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/c4f1bfe9-19b4-4451-95f7-3924bf9cc2b2/IGVFFI1935DBLW.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008565/",
"status": "released",
"term_name": "Illumina HiSeq 2500"
},
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin6hrs-FF2-BinF-PCR2-Rep1_S312_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0256YXOJ/",
"accession": "IGVFFI0256YXOJ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF2-BinF-PCR4-Rep1_S330"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:31:43.549118+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI0256YXOJ/@@download/IGVFFI0256YXOJ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/f3d79659-52ea-46da-bdae-744f2ee39782/IGVFFI0256YXOJ.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF2-BinF-PCR4-Rep1_S330.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI8971PQCM/",
"accession": "IGVFFI8971PQCM",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF2-BinF-PCR3-Rep1_S324"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:44:01.287728+00:00",
"file_format": "fastq",
"file_size": 30900481,
"href": "/sequence-files/IGVFFI8971PQCM/@@download/IGVFFI8971PQCM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/2f4fa433-abde-41eb-a61f-1377af9011d6/IGVFFI8971PQCM.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008565/",
"status": "released",
"term_name": "Illumina HiSeq 2500"
},
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin6hrs-FF2-BinF-PCR3-Rep1_S324_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS1569RNPD/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"notes": "The readout 2e41e624-f6c7-4f0c-a07e-bc36cefdca39 was removed from this measurement set.",
"preferred_assay_title": "CRISPR FlowFISH screen",
"protocols": [
"https://www.protocols.io/view/crispri-of-regulatory-elements-upon-degron-operati-5jyl82d59l2w/v1"
],
"release_timestamp": "2024-07-10T19:39:51.369584+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0402MSVI/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0402MSVI",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF2-BinF-PCR1-Rep1_S306",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF2-BinF-PCR2-Rep1_S312",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF2-BinF-PCR3-Rep1_S324",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF2-BinF-PCR4-Rep1_S330"
],
"classifications": [
"cell line"
],
"institutional_certificates": [],
"modifications": [
{
"@id": "/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/",
"modality": "degradation",
"status": "released"
},
{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
"modality": "interference",
"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": "Homo sapiens (male) HCT116 cell line (sorting details: FACS bin F for 80-100% expression of CCND1) treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours, modified with AID system targeting RAD21, CRISPRi Sp-dCas9-KOX1-KRAB, transfected with a guide library",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/",
"purpose": "activation",
"status": "released",
"summary": "Treatment of 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours",
"treatment_type": "chemical"
}
]
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-01T01:43:26.766525+00:00",
"summary": "mixed CRISPR FlowFISH screen sorted on the expression of CCND1 integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"targeted_genes": [
{
"@id": "/genes/ENSG00000110092/",
"geneid": "ENSG00000110092",
"name": "cyclin D1",
"status": "released",
"symbol": "CCND1",
"synonyms": [
"U21B31",
"cyclin D1",
"B-cell CLL/lymphoma 1",
"PRAD1 oncogene",
"PRAD1",
"CCND1",
"G1/S-specific cyclin-D1",
"BCL-1 oncogene",
"BCL1",
"D11S287E",
"B-cell lymphoma 1 protein"
]
}
],
"uuid": "b22868f5-ee13-47c3-b5af-22eadf5d726f"
}