{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5572SQRK/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5572SQRK",
"aliases": [
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR1-Rep1_S242",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR2-Rep1_S248",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR3-Rep1_S284",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR4-Rep1_S290"
],
"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": "Auxiliary set [IGVFDS6842FAIJ](/auxiliary-sets/IGVFDS6842FAIJ/) 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/IGVFDS6842FAIJ/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM5255ABUW](/in-vitro-systems/IGVFSM5255ABUW/) 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/IGVFSM5255ABUW/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS5572SQRK](/measurement-sets/IGVFDS5572SQRK/) 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/IGVFDS5572SQRK/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS5572SQRK](/measurement-sets/IGVFDS5572SQRK/) has sequence file(s) [IGVFFI8211KHIX](/sequence-files/IGVFFI8211KHIX/), [IGVFFI1781YSJE](/sequence-files/IGVFFI1781YSJE/), [IGVFFI4348ZUXP](/sequence-files/IGVFFI4348ZUXP/), [IGVFFI0056ZWFB](/sequence-files/IGVFFI0056ZWFB/) 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/IGVFDS5572SQRK/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM5255ABUW](/in-vitro-systems/IGVFSM5255ABUW/) 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/IGVFSM5255ABUW/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS6842FAIJ/",
"accession": "IGVFDS6842FAIJ",
"aliases": [
"jesse-engreitz:auxiliary_sortparams_CRUDO_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/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": "2024-05-13T22:16:36.585239+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/IGVFFI8434JLTQ/",
"accession": "IGVFFI8434JLTQ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR2-Rep1_S248"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:30:08.700092+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI8434JLTQ/@@download/IGVFFI8434JLTQ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/43656b07-a9ab-4829-af23-2074e998d577/IGVFFI8434JLTQ.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF1-BinB-PCR2-Rep1_S248.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI6541RIBO/",
"accession": "IGVFFI6541RIBO",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR1-Rep1_S242"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:29:54.459004+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI6541RIBO/@@download/IGVFFI6541RIBO.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/8eee4e1c-1f92-412c-acb1-2a58e5765bd8/IGVFFI6541RIBO.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF1-BinB-PCR1-Rep1_S242.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI4045SHGK/",
"accession": "IGVFFI4045SHGK",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR3-Rep1_S284"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:30:22.769115+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI4045SHGK/@@download/IGVFFI4045SHGK.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/5966239d-b340-48b5-bb4a-e74b887e9bdd/IGVFFI4045SHGK.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF1-BinB-PCR3-Rep1_S284.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI2535ZPBT/",
"accession": "IGVFFI2535ZPBT",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR4-Rep1_S290"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:30:37.235850+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI2535ZPBT/@@download/IGVFFI2535ZPBT.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/8986029e-5350-4d78-9a14-df02923f1b0a/IGVFFI2535ZPBT.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF1-BinB-PCR4-Rep1_S290.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI8211KHIX/",
"accession": "IGVFFI8211KHIX",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR4-Rep1_S290"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:42:55.899195+00:00",
"file_format": "fastq",
"file_size": 23445132,
"href": "/sequence-files/IGVFFI8211KHIX/@@download/IGVFFI8211KHIX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/d540256b-ab1d-4792-b9c0-5388c9cd4df6/IGVFFI8211KHIX.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-FF1-BinB-PCR4-Rep1_S290_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1781YSJE/",
"accession": "IGVFFI1781YSJE",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR3-Rep1_S284"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:42:38.091546+00:00",
"file_format": "fastq",
"file_size": 33923038,
"href": "/sequence-files/IGVFFI1781YSJE/@@download/IGVFFI1781YSJE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/3541381a-a7d4-4405-8ea4-244223aee743/IGVFFI1781YSJE.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-FF1-BinB-PCR3-Rep1_S284_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4348ZUXP/",
"accession": "IGVFFI4348ZUXP",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR1-Rep1_S242"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:42:03.750959+00:00",
"file_format": "fastq",
"file_size": 21187778,
"href": "/sequence-files/IGVFFI4348ZUXP/@@download/IGVFFI4348ZUXP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/918f39a3-4639-47fb-a14e-4729d40df862/IGVFFI4348ZUXP.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-FF1-BinB-PCR1-Rep1_S242_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0056ZWFB/",
"accession": "IGVFFI0056ZWFB",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR2-Rep1_S248"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:42:21.490730+00:00",
"file_format": "fastq",
"file_size": 15476191,
"href": "/sequence-files/IGVFFI0056ZWFB/@@download/IGVFFI0056ZWFB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/3f8af430-a4cd-4b6f-9ac6-caca93fce82b/IGVFFI0056ZWFB.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-FF1-BinB-PCR2-Rep1_S248_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": "2024-07-10T19:39:09.477001+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5255ABUW/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5255ABUW",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR1-Rep1_S242",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR2-Rep1_S248",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR3-Rep1_S284",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR4-Rep1_S290"
],
"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": "2024-06-01T01:42:03.750959+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": "7ea9bc0d-ca27-4f3e-8598-c347c68c0a36"
}