{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6786ONEQ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6786ONEQ",
"aliases": [
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF2-BinB-PCR1-Rep1_S302",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF2-BinB-PCR2-Rep1_S308",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF2-BinB-PCR3-Rep1_S320",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF2-BinB-PCR4-Rep1_S326"
],
"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 [IGVFDS6786ONEQ](/measurement-sets/IGVFDS6786ONEQ/) 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/IGVFDS6786ONEQ/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS6786ONEQ](/measurement-sets/IGVFDS6786ONEQ/) has sequence file(s) [IGVFFI8424NIOW](/sequence-files/IGVFFI8424NIOW/), [IGVFFI1340BULZ](/sequence-files/IGVFFI1340BULZ/), [IGVFFI7780IFRA](/sequence-files/IGVFFI7780IFRA/), [IGVFFI8500YXBS](/sequence-files/IGVFFI8500YXBS/) 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/IGVFDS6786ONEQ/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM7955GCNG](/in-vitro-systems/IGVFSM7955GCNG/) 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/IGVFSM7955GCNG/"
},
{
"category": "missing publication",
"detail": "Auxiliary set [IGVFDS1065WJDZ](/auxiliary-sets/IGVFDS1065WJDZ/) 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/IGVFDS1065WJDZ/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM7955GCNG](/in-vitro-systems/IGVFSM7955GCNG/) 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/IGVFSM7955GCNG/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS1065WJDZ/",
"accession": "IGVFDS1065WJDZ",
"aliases": [
"jesse-engreitz:auxiliary_sortparams_CRUDO_CCND1_Auxin6hrs-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": "2024-05-13T22:16:56.767863+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/IGVFFI2952SHUJ/",
"accession": "IGVFFI2952SHUJ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF2-BinB-PCR2-Rep1_S308"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:31:04.820734+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI2952SHUJ/@@download/IGVFFI2952SHUJ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/1faa7e09-a4a6-4d23-a566-18148c2314e9/IGVFFI2952SHUJ.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF2-BinB-PCR2-Rep1_S308.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI8424NIOW/",
"accession": "IGVFFI8424NIOW",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF2-BinB-PCR2-Rep1_S308"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:43:32.499378+00:00",
"file_format": "fastq",
"file_size": 16731168,
"href": "/sequence-files/IGVFFI8424NIOW/@@download/IGVFFI8424NIOW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/5f144e41-3596-4f79-a745-0e2d6c395881/IGVFFI8424NIOW.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-BinB-PCR2-Rep1_S308_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7387BMJH/",
"accession": "IGVFFI7387BMJH",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF2-BinB-PCR3-Rep1_S320"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:31:19.253449+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI7387BMJH/@@download/IGVFFI7387BMJH.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/2928fe46-61aa-4e46-b8ab-0a237ee6d35d/IGVFFI7387BMJH.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF2-BinB-PCR3-Rep1_S320.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI1008OIFS/",
"accession": "IGVFFI1008OIFS",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF2-BinB-PCR1-Rep1_S302"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:30:51.009122+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI1008OIFS/@@download/IGVFFI1008OIFS.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/4f69750d-2944-41f0-9151-39ffd0863888/IGVFFI1008OIFS.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF2-BinB-PCR1-Rep1_S302.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI3057FCLW/",
"accession": "IGVFFI3057FCLW",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF2-BinB-PCR4-Rep1_S326"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:31:33.176226+00:00",
"file_format": "yaml",
"file_size": 916,
"href": "/configuration-files/IGVFFI3057FCLW/@@download/IGVFFI3057FCLW.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/5ac68750-e0ad-44a6-9a46-c3dc55b72640/IGVFFI3057FCLW.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF2-BinB-PCR4-Rep1_S326.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI1340BULZ/",
"accession": "IGVFFI1340BULZ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF2-BinB-PCR4-Rep1_S326"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:44:07.106991+00:00",
"file_format": "fastq",
"file_size": 29976047,
"href": "/sequence-files/IGVFFI1340BULZ/@@download/IGVFFI1340BULZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/ff8c0e26-151c-453a-8360-b604e35c9480/IGVFFI1340BULZ.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-BinB-PCR4-Rep1_S326_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7780IFRA/",
"accession": "IGVFFI7780IFRA",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF2-BinB-PCR3-Rep1_S320"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:43:49.594143+00:00",
"file_format": "fastq",
"file_size": 21374840,
"href": "/sequence-files/IGVFFI7780IFRA/@@download/IGVFFI7780IFRA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/dab97557-02b5-4958-b755-fb3673c0f1d4/IGVFFI7780IFRA.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-BinB-PCR3-Rep1_S320_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8500YXBS/",
"accession": "IGVFFI8500YXBS",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF2-BinB-PCR1-Rep1_S302"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:43:15.474849+00:00",
"file_format": "fastq",
"file_size": 14684849,
"href": "/sequence-files/IGVFFI8500YXBS/@@download/IGVFFI8500YXBS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/6c08b6c5-e450-4658-9c0f-018326524737/IGVFFI8500YXBS.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-BinB-PCR1-Rep1_S302_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": "2024-07-10T19:39:34.404210+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7955GCNG/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7955GCNG",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF2-BinB-PCR1-Rep1_S302",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF2-BinB-PCR2-Rep1_S308",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF2-BinB-PCR3-Rep1_S320",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF2-BinB-PCR4-Rep1_S326"
],
"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 B for 10-20% 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": "2024-06-01T01:43:15.474849+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": "81e91c32-3796-41a0-a26f-e3b69450ec11"
}