{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3585LXSG/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3585LXSG",
"aliases": [
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF2-BinC-PCR1-Rep1_S231",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF2-BinC-PCR2-Rep1_S237",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF2-BinC-PCR3-Rep1_S273",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF2-BinC-PCR4-Rep1_S279"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"assay_slims": [
"CRISPR screens"
],
"status": "released",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS3585LXSG](/measurement-sets/IGVFDS3585LXSG/) 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/IGVFDS3585LXSG/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS3585LXSG](/measurement-sets/IGVFDS3585LXSG/) has sequence file(s) [IGVFFI6700LZGL](/sequence-files/IGVFFI6700LZGL/), [IGVFFI8964HZGC](/sequence-files/IGVFFI8964HZGC/), [IGVFFI3279BRAW](/sequence-files/IGVFFI3279BRAW/), [IGVFFI2646XUWX](/sequence-files/IGVFFI2646XUWX/) 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/IGVFDS3585LXSG/"
},
{
"category": "missing publication",
"detail": "Auxiliary set [IGVFDS1549RKIJ](/auxiliary-sets/IGVFDS1549RKIJ/) 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": "/auxiliary-sets/IGVFDS1549RKIJ/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM2887QEDU](/in-vitro-systems/IGVFSM2887QEDU/) 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/IGVFSM2887QEDU/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM2887QEDU](/in-vitro-systems/IGVFSM2887QEDU/) 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/IGVFSM2887QEDU/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS1549RKIJ/",
"accession": "IGVFDS1549RKIJ",
"aliases": [
"jesse-engreitz:auxiliary_sortparams_CRUDO_CCND1_Auxin0hrs-FF2"
],
"file_set_type": "cell sorting",
"status": "released"
}
],
"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": "2024-05-13T22:07:47.854187+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/IGVFFI2309WPWB/",
"accession": "IGVFFI2309WPWB",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF2-BinC-PCR3-Rep1_S273"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:29:28.956831+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI2309WPWB/@@download/IGVFFI2309WPWB.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/5fd58b14-e08b-4494-8c7e-9e1211f081c6/IGVFFI2309WPWB.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF2-BinC-PCR3-Rep1_S273.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI8143HFAY/",
"accession": "IGVFFI8143HFAY",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF2-BinC-PCR4-Rep1_S279"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:29:42.980624+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI8143HFAY/@@download/IGVFFI8143HFAY.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/820c632f-f067-4dae-8dd7-dae372599235/IGVFFI8143HFAY.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF2-BinC-PCR4-Rep1_S279.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI7248KXML/",
"accession": "IGVFFI7248KXML",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF2-BinC-PCR2-Rep1_S237"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:29:15.053829+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI7248KXML/@@download/IGVFFI7248KXML.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/ffcaefcc-07ac-4517-9540-6fa2f704464c/IGVFFI7248KXML.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF2-BinC-PCR2-Rep1_S237.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI8487XWZG/",
"accession": "IGVFFI8487XWZG",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF2-BinC-PCR1-Rep1_S231"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:29:01.061087+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI8487XWZG/@@download/IGVFFI8487XWZG.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/17daaef4-9cbd-42bc-9fa7-ef20c29d8da3/IGVFFI8487XWZG.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF2-BinC-PCR1-Rep1_S231.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI6700LZGL/",
"accession": "IGVFFI6700LZGL",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF2-BinC-PCR1-Rep1_S231"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:37:14.548770+00:00",
"file_format": "fastq",
"file_size": 20627639,
"href": "/sequence-files/IGVFFI6700LZGL/@@download/IGVFFI6700LZGL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/e49d62e5-e59c-4338-84a0-0e6de3db5505/IGVFFI6700LZGL.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-Auxin0hrs-FF2-BinC-PCR1-Rep1_S231_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8964HZGC/",
"accession": "IGVFFI8964HZGC",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF2-BinC-PCR2-Rep1_S237"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:37:32.399347+00:00",
"file_format": "fastq",
"file_size": 20753788,
"href": "/sequence-files/IGVFFI8964HZGC/@@download/IGVFFI8964HZGC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/7cc49950-05f0-4d84-b41c-6155064af49d/IGVFFI8964HZGC.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-Auxin0hrs-FF2-BinC-PCR2-Rep1_S237_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3279BRAW/",
"accession": "IGVFFI3279BRAW",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF2-BinC-PCR4-Rep1_S279"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:38:12.527386+00:00",
"file_format": "fastq",
"file_size": 21998916,
"href": "/sequence-files/IGVFFI3279BRAW/@@download/IGVFFI3279BRAW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/af68bf52-73c6-4b69-8dc9-04397702003b/IGVFFI3279BRAW.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-Auxin0hrs-FF2-BinC-PCR4-Rep1_S279_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2646XUWX/",
"accession": "IGVFFI2646XUWX",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF2-BinC-PCR3-Rep1_S273"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:37:50.090507+00:00",
"file_format": "fastq",
"file_size": 27116432,
"href": "/sequence-files/IGVFFI2646XUWX/@@download/IGVFFI2646XUWX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/47fa3575-ac68-470f-8ab7-437ce659a2ab/IGVFFI2646XUWX.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-Auxin0hrs-FF2-BinC-PCR3-Rep1_S273_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": "2024-07-10T19:38:47.963631+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2887QEDU/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2887QEDU",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF2-BinC-PCR1-Rep1_S231",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF2-BinC-PCR2-Rep1_S237",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF2-BinC-PCR3-Rep1_S273",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF2-BinC-PCR4-Rep1_S279"
],
"classifications": [
"cell line"
],
"institutional_certificates": [],
"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": "Homo sapiens (male) HCT116 cell line (sorting details: FACS bin C for 35-45% expression of CCND1) modified with CRISPRi Sp-dCas9-KOX1-KRAB, inactive AID system targeting RAD21, transfected with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-01T01:37:14.548770+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": "7e7bfa0f-2340-44d3-900e-994e5ed4a23b"
}