{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0483TWVD/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0483TWVD",
"aliases": [
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinE-PCR1-Rep1_S221",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinE-PCR2-Rep1_S227",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinE-PCR3-Rep1_S263",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinE-PCR4-Rep1_S269"
],
"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 [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": "Measurement set [IGVFDS0483TWVD](/measurement-sets/IGVFDS0483TWVD/) 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/IGVFDS0483TWVD/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS0483TWVD](/measurement-sets/IGVFDS0483TWVD/) has sequence file(s) [IGVFFI5265HDML](/sequence-files/IGVFFI5265HDML/), [IGVFFI6923AOHM](/sequence-files/IGVFFI6923AOHM/), [IGVFFI2029EJDA](/sequence-files/IGVFFI2029EJDA/), [IGVFFI2708TQVM](/sequence-files/IGVFFI2708TQVM/) 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/IGVFDS0483TWVD/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM7928IVYJ](/in-vitro-systems/IGVFSM7928IVYJ/) 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/IGVFSM7928IVYJ/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM7928IVYJ](/in-vitro-systems/IGVFSM7928IVYJ/) 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/IGVFSM7928IVYJ/"
}
]
},
"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": "2024-05-13T22:07:25.438060+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/IGVFFI4701OROT/",
"accession": "IGVFFI4701OROT",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF1-BinE-PCR1-Rep1_S221"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:28:08.248111+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI4701OROT/@@download/IGVFFI4701OROT.yaml.gz",
"md5sum": "1af57331c0cd0e32d99f9f04ba9a1ee3",
"s3_uri": "s3://igvf-files/2024/06/11/a5017d72-9c2f-4441-bed4-60b0b2fe0508/IGVFFI4701OROT.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF1-BinE-PCR1-Rep1_S221.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI6041XGLZ/",
"accession": "IGVFFI6041XGLZ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF1-BinE-PCR3-Rep1_S263"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:28:36.427359+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI6041XGLZ/@@download/IGVFFI6041XGLZ.yaml.gz",
"md5sum": "c07070cb962062b8b2772c2dd97fbd4c",
"s3_uri": "s3://igvf-files/2024/06/11/d4694a35-e535-460c-a4f2-225039e35249/IGVFFI6041XGLZ.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF1-BinE-PCR3-Rep1_S263.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI4030NNGD/",
"accession": "IGVFFI4030NNGD",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF1-BinE-PCR4-Rep1_S269"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:28:50.887941+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI4030NNGD/@@download/IGVFFI4030NNGD.yaml.gz",
"md5sum": "271be08987b73b6815ca38a5f2c4e2a1",
"s3_uri": "s3://igvf-files/2024/06/11/b1998582-56ca-4704-b7ad-3f2c8731ea94/IGVFFI4030NNGD.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF1-BinE-PCR4-Rep1_S269.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI6175WMTN/",
"accession": "IGVFFI6175WMTN",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF1-BinE-PCR2-Rep1_S227"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:28:22.695247+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI6175WMTN/@@download/IGVFFI6175WMTN.yaml.gz",
"md5sum": "a8e74024245cd87af37417e171d0bb67",
"s3_uri": "s3://igvf-files/2024/06/11/81754be6-596c-4da6-9cbd-ce6e2f3581ab/IGVFFI6175WMTN.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF1-BinE-PCR2-Rep1_S227.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI5265HDML/",
"accession": "IGVFFI5265HDML",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF1-BinE-PCR2-Rep1_S227"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:36:26.573714+00:00",
"file_format": "fastq",
"file_size": 23690903,
"href": "/sequence-files/IGVFFI5265HDML/@@download/IGVFFI5265HDML.fastq.gz",
"md5sum": "98e8c65bd44ff1993eccab738fe46656",
"s3_uri": "s3://igvf-files/2024/06/01/eee9f83f-21f4-403e-99c0-d71e48e1b3de/IGVFFI5265HDML.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-BinE-PCR2-Rep1_S227_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6923AOHM/",
"accession": "IGVFFI6923AOHM",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF1-BinE-PCR3-Rep1_S263"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:36:44.490071+00:00",
"file_format": "fastq",
"file_size": 23912351,
"href": "/sequence-files/IGVFFI6923AOHM/@@download/IGVFFI6923AOHM.fastq.gz",
"md5sum": "74bece449e93979c097338fe931b6e7c",
"s3_uri": "s3://igvf-files/2024/06/01/b521a48f-622c-453f-b701-58e1a125eee8/IGVFFI6923AOHM.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-BinE-PCR3-Rep1_S263_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2029EJDA/",
"accession": "IGVFFI2029EJDA",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF1-BinE-PCR1-Rep1_S221"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:36:08.251542+00:00",
"file_format": "fastq",
"file_size": 24285695,
"href": "/sequence-files/IGVFFI2029EJDA/@@download/IGVFFI2029EJDA.fastq.gz",
"md5sum": "8ad83d74057bdede7f0fdab426cc7901",
"s3_uri": "s3://igvf-files/2024/06/01/83a101d2-954b-4196-a109-8cecea0854ec/IGVFFI2029EJDA.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-BinE-PCR1-Rep1_S221_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2708TQVM/",
"accession": "IGVFFI2708TQVM",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF1-BinE-PCR4-Rep1_S269"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:37:02.676989+00:00",
"file_format": "fastq",
"file_size": 29419732,
"href": "/sequence-files/IGVFFI2708TQVM/@@download/IGVFFI2708TQVM.fastq.gz",
"md5sum": "f24a9986ba0237ac026546e574575194",
"s3_uri": "s3://igvf-files/2024/06/01/42679afd-b299-4aaf-8f93-9f3a3c51a483/IGVFFI2708TQVM.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-BinE-PCR4-Rep1_S269_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": "2024-07-10T19:38:31.319165+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7928IVYJ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7928IVYJ",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinE-PCR1-Rep1_S221",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinE-PCR2-Rep1_S227",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinE-PCR3-Rep1_S263",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinE-PCR4-Rep1_S269"
],
"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 E for 80-90% 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": "2024-06-01T01:36:08.251542+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": "49084d56-a991-4f36-a121-69754909a4bc"
}