{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6001NZOV/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6001NZOV",
"aliases": [
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinD-PCR1-Rep1_S220",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinD-PCR2-Rep1_S226",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinD-PCR3-Rep1_S262",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinD-PCR4-Rep1_S268"
],
"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 [IGVFDS6001NZOV](/measurement-sets/IGVFDS6001NZOV/) 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/IGVFDS6001NZOV/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS6001NZOV](/measurement-sets/IGVFDS6001NZOV/) has sequence file(s) [IGVFFI9404GXRL](/sequence-files/IGVFFI9404GXRL/), [IGVFFI9086AHHC](/sequence-files/IGVFFI9086AHHC/), [IGVFFI1781AOFZ](/sequence-files/IGVFFI1781AOFZ/), [IGVFFI0907KKUJ](/sequence-files/IGVFFI0907KKUJ/) 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/IGVFDS6001NZOV/"
},
{
"category": "missing publication",
"detail": "Auxiliary set [IGVFDS5464XLTY](/auxiliary-sets/IGVFDS5464XLTY/) 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/IGVFDS5464XLTY/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM6400EVKX](/in-vitro-systems/IGVFSM6400EVKX/) 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/IGVFSM6400EVKX/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM6400EVKX](/in-vitro-systems/IGVFSM6400EVKX/) 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/IGVFSM6400EVKX/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS5464XLTY/",
"accession": "IGVFDS5464XLTY",
"aliases": [
"jesse-engreitz:auxiliary_sortparams_CRUDO_CCND1_Auxin0hrs-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": "2024-05-13T22:07:24.564050+00:00",
"data_use_limitation_summaries": [
"no certificate"
],
"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/IGVFFI2555BDBO/",
"accession": "IGVFFI2555BDBO",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF1-BinD-PCR4-Rep1_S268"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:28:48.641839+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI2555BDBO/@@download/IGVFFI2555BDBO.yaml.gz",
"md5sum": "77107f1ea0c6c031beb874a5b49789bc",
"s3_uri": "s3://igvf-files/2024/06/11/3c05c298-11ef-4044-b3a7-cce09cefaeee/IGVFFI2555BDBO.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF1-BinD-PCR4-Rep1_S268.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI7168PSKZ/",
"accession": "IGVFFI7168PSKZ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF1-BinD-PCR1-Rep1_S220"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:28:05.671236+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI7168PSKZ/@@download/IGVFFI7168PSKZ.yaml.gz",
"md5sum": "be635b3f8e963479ddd63c64b788af5a",
"s3_uri": "s3://igvf-files/2024/06/11/48f35b37-3419-4608-8394-8f2582c6d7cc/IGVFFI7168PSKZ.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF1-BinD-PCR1-Rep1_S220.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI8614RUON/",
"accession": "IGVFFI8614RUON",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF1-BinD-PCR3-Rep1_S262"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:28:34.197831+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI8614RUON/@@download/IGVFFI8614RUON.yaml.gz",
"md5sum": "4e425ac24a70de3d4f8ec3df7e8d22fb",
"s3_uri": "s3://igvf-files/2024/06/11/247c4f9a-83cb-4d88-adc3-67f9bb4a185f/IGVFFI8614RUON.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF1-BinD-PCR3-Rep1_S262.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI9404GXRL/",
"accession": "IGVFFI9404GXRL",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF1-BinD-PCR4-Rep1_S268"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:36:59.616473+00:00",
"file_format": "fastq",
"file_size": 27021538,
"href": "/sequence-files/IGVFFI9404GXRL/@@download/IGVFFI9404GXRL.fastq.gz",
"md5sum": "efcdc0fae8d9f2cf23b043548c102660",
"s3_uri": "s3://igvf-files/2024/06/01/95f3ceb1-5fd9-4ac7-9a17-e47e4aedfdbb/IGVFFI9404GXRL.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-FF1-BinD-PCR4-Rep1_S268_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2589FZCK/",
"accession": "IGVFFI2589FZCK",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF1-BinD-PCR2-Rep1_S226"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:28:20.413329+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI2589FZCK/@@download/IGVFFI2589FZCK.yaml.gz",
"md5sum": "0d4791f45e274bbdf85127b7adc0a0b9",
"s3_uri": "s3://igvf-files/2024/06/11/180090c9-a798-4361-a0e3-740dedf0aa51/IGVFFI2589FZCK.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF1-BinD-PCR2-Rep1_S226.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI9086AHHC/",
"accession": "IGVFFI9086AHHC",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF1-BinD-PCR2-Rep1_S226"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:36:23.174986+00:00",
"file_format": "fastq",
"file_size": 22613096,
"href": "/sequence-files/IGVFFI9086AHHC/@@download/IGVFFI9086AHHC.fastq.gz",
"md5sum": "6a048814aa9f3c88ed9ea1c077c1354e",
"s3_uri": "s3://igvf-files/2024/06/01/1247aa3a-d668-4e79-84f4-e12a1c3c4553/IGVFFI9086AHHC.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-FF1-BinD-PCR2-Rep1_S226_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1781AOFZ/",
"accession": "IGVFFI1781AOFZ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF1-BinD-PCR1-Rep1_S220"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:36:05.323690+00:00",
"file_format": "fastq",
"file_size": 23853924,
"href": "/sequence-files/IGVFFI1781AOFZ/@@download/IGVFFI1781AOFZ.fastq.gz",
"md5sum": "0b3db9029cf51a2273b23da0428a68e6",
"s3_uri": "s3://igvf-files/2024/06/01/07b651f1-1ba7-41ba-b6b0-e26e31e77c99/IGVFFI1781AOFZ.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-FF1-BinD-PCR1-Rep1_S220_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0907KKUJ/",
"accession": "IGVFFI0907KKUJ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF1-BinD-PCR3-Rep1_S262"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:36:41.470464+00:00",
"file_format": "fastq",
"file_size": 30315346,
"href": "/sequence-files/IGVFFI0907KKUJ/@@download/IGVFFI0907KKUJ.fastq.gz",
"md5sum": "ffd571e70d887133a1460616167568f6",
"s3_uri": "s3://igvf-files/2024/06/01/a7a98b1a-9c08-4341-ba00-990a987c698b/IGVFFI0907KKUJ.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-FF1-BinD-PCR3-Rep1_S262_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": "2024-07-10T19:38:27.079780+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM6400EVKX/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6400EVKX",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinD-PCR1-Rep1_S220",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinD-PCR2-Rep1_S226",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinD-PCR3-Rep1_S262",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinD-PCR4-Rep1_S268"
],
"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 D for 55-65% 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": "2024-06-01T01:36:05.323690+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": "2274e3a8-261c-45d3-ba9f-0ecd579e79f4"
}