{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2079MGOR/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2079MGOR",
"aliases": [
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinF-PCR1_S6",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinF-PCR2_S102",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinF-PCR3_S198",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinF-PCR4_S294"
],
"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": "In vitro system [IGVFSM0904FNLS](/in-vitro-systems/IGVFSM0904FNLS/) 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/IGVFSM0904FNLS/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS2079MGOR](/measurement-sets/IGVFDS2079MGOR/) 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/IGVFDS2079MGOR/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS2079MGOR](/measurement-sets/IGVFDS2079MGOR/) has sequence file(s) [IGVFFI5705VZDO](/sequence-files/IGVFFI5705VZDO/), [IGVFFI5243ZITD](/sequence-files/IGVFFI5243ZITD/), [IGVFFI3706DIIS](/sequence-files/IGVFFI3706DIIS/), [IGVFFI1185QZTN](/sequence-files/IGVFFI1185QZTN/) 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/IGVFDS2079MGOR/"
},
{
"category": "missing publication",
"detail": "Auxiliary set [IGVFDS5877TZTD](/auxiliary-sets/IGVFDS5877TZTD/) 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/IGVFDS5877TZTD/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM0904FNLS](/in-vitro-systems/IGVFSM0904FNLS/) 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/IGVFSM0904FNLS/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS5877TZTD/",
"accession": "IGVFDS5877TZTD",
"aliases": [
"jesse-engreitz:auxiliary_sortparams_CRUDO_PILOT_CCND1-Auxin6hrs-FF1"
],
"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/IGVFDS0392OWNZ/",
"accession": "IGVFDS0392OWNZ",
"file_set_type": "guide library",
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI4981YFMT/",
"accession": "IGVFFI4981YFMT",
"content_type": "guide RNA sequences",
"status": "released",
"summary": "GRCh38 guide RNA sequences"
}
],
"status": "released",
"summary": "guide (sgRNA) library targeting accessible genome regions in 36 genomic loci"
}
],
"control_for": [],
"creation_timestamp": "2024-05-06T22:19:10.178669+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/IGVFFI8851ZPDX/",
"accession": "IGVFFI8851ZPDX",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinF-PCR1_S6"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:23:05.209946+00:00",
"file_format": "yaml",
"file_size": 906,
"href": "/configuration-files/IGVFFI8851ZPDX/@@download/IGVFFI8851ZPDX.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/5c748d96-94a4-4dba-9697-f23f81e0e261/IGVFFI8851ZPDX.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin6hrs-FF1-BinF-PCR1_S6.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI7044YYIY/",
"accession": "IGVFFI7044YYIY",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinF-PCR4_S294"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:23:46.211814+00:00",
"file_format": "yaml",
"file_size": 910,
"href": "/configuration-files/IGVFFI7044YYIY/@@download/IGVFFI7044YYIY.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/77b66746-a2c4-47a4-abba-696f2f49308a/IGVFFI7044YYIY.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin6hrs-FF1-BinF-PCR4_S294.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI1848XHZT/",
"accession": "IGVFFI1848XHZT",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinF-PCR3_S198"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:23:32.494764+00:00",
"file_format": "yaml",
"file_size": 910,
"href": "/configuration-files/IGVFFI1848XHZT/@@download/IGVFFI1848XHZT.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/abb18ba0-39f9-4767-add3-8e8570bd93c1/IGVFFI1848XHZT.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin6hrs-FF1-BinF-PCR3_S198.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI5705VZDO/",
"accession": "IGVFFI5705VZDO",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinF-PCR4_S294"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:25:40.430198+00:00",
"file_format": "fastq",
"file_size": 2578702,
"href": "/sequence-files/IGVFFI5705VZDO/@@download/IGVFFI5705VZDO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/07d52b45-2ff8-4287-8235-1a7219a20949/IGVFFI5705VZDO.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/210301B002-CohesinFF/fastq/CCND1-Auxin6hrs-FF1-BinF-PCR4_S294_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6893TRQO/",
"accession": "IGVFFI6893TRQO",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinF-PCR2_S102"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:23:18.957181+00:00",
"file_format": "yaml",
"file_size": 910,
"href": "/configuration-files/IGVFFI6893TRQO/@@download/IGVFFI6893TRQO.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/0d209287-25c9-4f63-beea-4152ec6c39fc/IGVFFI6893TRQO.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin6hrs-FF1-BinF-PCR2_S102.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI5243ZITD/",
"accession": "IGVFFI5243ZITD",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinF-PCR3_S198"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:25:24.889588+00:00",
"file_format": "fastq",
"file_size": 3289690,
"href": "/sequence-files/IGVFFI5243ZITD/@@download/IGVFFI5243ZITD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/a2365a59-3a2f-4313-9ba1-40510a005f41/IGVFFI5243ZITD.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/210301B002-CohesinFF/fastq/CCND1-Auxin6hrs-FF1-BinF-PCR3_S198_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3706DIIS/",
"accession": "IGVFFI3706DIIS",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinF-PCR1_S6"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:24:52.604345+00:00",
"file_format": "fastq",
"file_size": 2386043,
"href": "/sequence-files/IGVFFI3706DIIS/@@download/IGVFFI3706DIIS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/89def70c-55ca-4878-934a-abff7fb08ffb/IGVFFI3706DIIS.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/210301B002-CohesinFF/fastq/CCND1-Auxin6hrs-FF1-BinF-PCR1_S6_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1185QZTN/",
"accession": "IGVFFI1185QZTN",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinF-PCR2_S102"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:25:08.876707+00:00",
"file_format": "fastq",
"file_size": 2949646,
"href": "/sequence-files/IGVFFI1185QZTN/@@download/IGVFFI1185QZTN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/958be19b-e16b-4675-8ca8-d9fe31289887/IGVFFI1185QZTN.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/210301B002-CohesinFF/fastq/CCND1-Auxin6hrs-FF1-BinF-PCR2_S102_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS2982SJGW/"
],
"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": "2024-07-10T19:50:35.624658+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0904FNLS/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0904FNLS",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinF-PCR1_S6",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinF-PCR2_S102",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinF-PCR3_S198",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinF-PCR4_S294"
],
"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": "2024-06-01T01:24:52.604345+00:00",
"summary": "mixed CRISPR FlowFISH screen sorted on the expression of CCND1 integrating a guide (sgRNA) library targeting accessible genome regions in 36 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": "dbdffbc6-9cae-4749-acaf-143e8ab83163"
}