{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8571HTVZ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8571HTVZ",
"aliases": [
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinC-PCR1_S3",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinC-PCR2_S99",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinC-PCR3_S195",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinC-PCR4_S291"
],
"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 [IGVFDS8571HTVZ](/measurement-sets/IGVFDS8571HTVZ/) 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/IGVFDS8571HTVZ/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS8571HTVZ](/measurement-sets/IGVFDS8571HTVZ/) has sequence file(s) [IGVFFI2761AOAR](/sequence-files/IGVFFI2761AOAR/), [IGVFFI6827FMYI](/sequence-files/IGVFFI6827FMYI/), [IGVFFI2191UDNG](/sequence-files/IGVFFI2191UDNG/), [IGVFFI5612HJRS](/sequence-files/IGVFFI5612HJRS/) 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/IGVFDS8571HTVZ/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM6480FETB](/in-vitro-systems/IGVFSM6480FETB/) 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/IGVFSM6480FETB/"
},
{
"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 [IGVFSM6480FETB](/in-vitro-systems/IGVFSM6480FETB/) 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/IGVFSM6480FETB/"
}
]
},
"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": "2024-05-06T22:19:06.833888+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/IGVFFI9949JLMY/",
"accession": "IGVFFI9949JLMY",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinC-PCR4_S291"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:23:39.402440+00:00",
"file_format": "yaml",
"file_size": 910,
"href": "/configuration-files/IGVFFI9949JLMY/@@download/IGVFFI9949JLMY.yaml.gz",
"md5sum": "e8c0818cc73c96ceeeacb168b707974f",
"s3_uri": "s3://igvf-files/2024/06/11/ad6bc740-2d7a-43d6-8aa9-21d98f68bf64/IGVFFI9949JLMY.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin6hrs-FF1-BinC-PCR4_S291.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI0690VWRF/",
"accession": "IGVFFI0690VWRF",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinC-PCR3_S195"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:23:25.880187+00:00",
"file_format": "yaml",
"file_size": 908,
"href": "/configuration-files/IGVFFI0690VWRF/@@download/IGVFFI0690VWRF.yaml.gz",
"md5sum": "0693daf670f6fca9daaa1234dca34758",
"s3_uri": "s3://igvf-files/2024/06/11/b3a2a20f-17f6-4cf5-acd7-ec13c9c94a08/IGVFFI0690VWRF.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin6hrs-FF1-BinC-PCR3_S195.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI0324BUPW/",
"accession": "IGVFFI0324BUPW",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinC-PCR1_S3"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:22:57.717231+00:00",
"file_format": "yaml",
"file_size": 905,
"href": "/configuration-files/IGVFFI0324BUPW/@@download/IGVFFI0324BUPW.yaml.gz",
"md5sum": "4266d319f7ec4f849e3d4c137a4ebc92",
"s3_uri": "s3://igvf-files/2024/06/11/67c51a73-3d25-4928-8b9b-6dd17ef45258/IGVFFI0324BUPW.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin6hrs-FF1-BinC-PCR1_S3.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI2434JICM/",
"accession": "IGVFFI2434JICM",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinC-PCR2_S99"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:23:11.923535+00:00",
"file_format": "yaml",
"file_size": 907,
"href": "/configuration-files/IGVFFI2434JICM/@@download/IGVFFI2434JICM.yaml.gz",
"md5sum": "deb1a9ffef27b572d8881faa555cfde6",
"s3_uri": "s3://igvf-files/2024/06/11/1f38da5f-824d-4ce1-bcd6-c8a3f696b7fa/IGVFFI2434JICM.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin6hrs-FF1-BinC-PCR2_S99.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI2761AOAR/",
"accession": "IGVFFI2761AOAR",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinC-PCR1_S3"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:24:43.745452+00:00",
"file_format": "fastq",
"file_size": 5675294,
"href": "/sequence-files/IGVFFI2761AOAR/@@download/IGVFFI2761AOAR.fastq.gz",
"md5sum": "5471bea6726f973449e447c60f48c226",
"s3_uri": "s3://igvf-files/2024/06/01/f81224e2-392f-4f4d-8c12-36a03a779cfd/IGVFFI2761AOAR.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-BinC-PCR1_S3_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6827FMYI/",
"accession": "IGVFFI6827FMYI",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinC-PCR4_S291"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:25:32.354053+00:00",
"file_format": "fastq",
"file_size": 6899881,
"href": "/sequence-files/IGVFFI6827FMYI/@@download/IGVFFI6827FMYI.fastq.gz",
"md5sum": "0ac929663866ab118f34dc62ec3d4229",
"s3_uri": "s3://igvf-files/2024/06/01/b83ad32c-03aa-44b1-8361-9050ff2bb04a/IGVFFI6827FMYI.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-BinC-PCR4_S291_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2191UDNG/",
"accession": "IGVFFI2191UDNG",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinC-PCR2_S99"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:25:00.480408+00:00",
"file_format": "fastq",
"file_size": 7816883,
"href": "/sequence-files/IGVFFI2191UDNG/@@download/IGVFFI2191UDNG.fastq.gz",
"md5sum": "c7095abe1850403125a7d18a29bb915b",
"s3_uri": "s3://igvf-files/2024/06/01/6e1958c6-580f-4ff0-9fca-849d53cce21d/IGVFFI2191UDNG.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-BinC-PCR2_S99_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5612HJRS/",
"accession": "IGVFFI5612HJRS",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinC-PCR3_S195"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:25:16.926009+00:00",
"file_format": "fastq",
"file_size": 7863756,
"href": "/sequence-files/IGVFFI5612HJRS/@@download/IGVFFI5612HJRS.fastq.gz",
"md5sum": "4d9edd368672f01c240a7c297e794d28",
"s3_uri": "s3://igvf-files/2024/06/01/15c4c816-244b-48bc-8a25-c118caa67699/IGVFFI5612HJRS.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-BinC-PCR3_S195_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": "2024-07-10T19:50:12.936472+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM6480FETB/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6480FETB",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinC-PCR1_S3",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinC-PCR2_S99",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinC-PCR3_S195",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinC-PCR4_S291"
],
"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 C for 35-45% 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_term_name": "5-Phenyl-1H-indole-3-acetic acid",
"treatment_type": "chemical"
}
]
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-01T01:24:43.745452+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": "d80652d0-973c-4264-b91b-d4d4c55cbf80"
}