{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2980PYWE/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2980PYWE",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF1-BinD-PCR1_S4",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF1-BinD-PCR2_S10",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF1-BinD-PCR3_S100",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF1-BinD-PCR4_S106"
],
"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 [IGVFDS9621FJCZ](/auxiliary-sets/IGVFDS9621FJCZ/) 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/IGVFDS9621FJCZ/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS2980PYWE](/measurement-sets/IGVFDS2980PYWE/) 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/IGVFDS2980PYWE/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS2980PYWE](/measurement-sets/IGVFDS2980PYWE/) has sequence file(s) [IGVFFI4858BKOD](/sequence-files/IGVFFI4858BKOD/), [IGVFFI4264YACL](/sequence-files/IGVFFI4264YACL/), [IGVFFI8693SHGC](/sequence-files/IGVFFI8693SHGC/), [IGVFFI1744BOFQ](/sequence-files/IGVFFI1744BOFQ/) 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/IGVFDS2980PYWE/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM1425VIPO](/in-vitro-systems/IGVFSM1425VIPO/) 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/IGVFSM1425VIPO/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM1425VIPO](/in-vitro-systems/IGVFSM1425VIPO/) 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/IGVFSM1425VIPO/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS9621FJCZ/",
"accession": "IGVFDS9621FJCZ",
"aliases": [
"jesse-engreitz:auxiliary_sortparams_CRUDO_KITLG-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/IGVFDS7846UISG/",
"accession": "IGVFDS7846UISG",
"file_set_type": "guide library",
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI5995VHKI/",
"accession": "IGVFFI5995VHKI",
"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": "2024-05-16T17:32:32.383771+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/IGVFFI9274YGES/",
"accession": "IGVFFI9274YGES",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF1-BinD-PCR2_S10"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:06:01.372984+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI9274YGES/@@download/IGVFFI9274YGES.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/4e493946-2c99-4267-a417-4cefd95c8561/IGVFFI9274YGES.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF1-BinD-PCR2_S10.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI1010LWUE/",
"accession": "IGVFFI1010LWUE",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF1-BinD-PCR4_S106"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:06:28.377971+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI1010LWUE/@@download/IGVFFI1010LWUE.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/5acb3a44-d0b6-4ce7-badb-5751ab9eed50/IGVFFI1010LWUE.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF1-BinD-PCR4_S106.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI8666GJRR/",
"accession": "IGVFFI8666GJRR",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF1-BinD-PCR1_S4"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:05:47.815569+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI8666GJRR/@@download/IGVFFI8666GJRR.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/6fdfe852-db29-4621-9958-e3a6f3a2a6a2/IGVFFI8666GJRR.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF1-BinD-PCR1_S4.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI4858BKOD/",
"accession": "IGVFFI4858BKOD",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF1-BinD-PCR4_S106"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:11:19.463965+00:00",
"file_format": "fastq",
"file_size": 27644417,
"href": "/sequence-files/IGVFFI4858BKOD/@@download/IGVFFI4858BKOD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/957d04ee-9201-4cc0-a370-6977d4f8d637/IGVFFI4858BKOD.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/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF1-BinD-PCR4_S106_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3969UIVE/",
"accession": "IGVFFI3969UIVE",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF1-BinD-PCR3_S100"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:06:15.070180+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI3969UIVE/@@download/IGVFFI3969UIVE.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/4125b02e-d616-4195-9a6a-63a3acd3dc89/IGVFFI3969UIVE.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF1-BinD-PCR3_S100.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI4264YACL/",
"accession": "IGVFFI4264YACL",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF1-BinD-PCR1_S4"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:10:20.716827+00:00",
"file_format": "fastq",
"file_size": 9801888,
"href": "/sequence-files/IGVFFI4264YACL/@@download/IGVFFI4264YACL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/ab331184-e9cc-4b40-9871-b0fac0a4a787/IGVFFI4264YACL.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/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF1-BinD-PCR1_S4_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8693SHGC/",
"accession": "IGVFFI8693SHGC",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF1-BinD-PCR2_S10"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:10:43.232729+00:00",
"file_format": "fastq",
"file_size": 11756254,
"href": "/sequence-files/IGVFFI8693SHGC/@@download/IGVFFI8693SHGC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/bd764be1-b4cc-4e6d-8bf0-3829ad17890b/IGVFFI8693SHGC.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/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF1-BinD-PCR2_S10_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1744BOFQ/",
"accession": "IGVFFI1744BOFQ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF1-BinD-PCR3_S100"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:11:01.187618+00:00",
"file_format": "fastq",
"file_size": 29455156,
"href": "/sequence-files/IGVFFI1744BOFQ/@@download/IGVFFI1744BOFQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/7bf8b5c1-f25b-4e20-b489-bfde2ffa5c7b/IGVFFI1744BOFQ.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/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF1-BinD-PCR3_S100_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS6482AXWW/"
],
"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": "2024-07-10T19:42:10.863727+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1425VIPO/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1425VIPO",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF1-BinD-PCR1_S4",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF1-BinD-PCR2_S10",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF1-BinD-PCR3_S100",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF1-BinD-PCR4_S106"
],
"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 KITLG) 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": "2024-06-01T02:10:20.716827+00:00",
"summary": "mixed CRISPR FlowFISH screen sorted on the expression of KITLG integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"targeted_genes": [
{
"@id": "/genes/ENSG00000049130/",
"geneid": "ENSG00000049130",
"name": "KIT ligand",
"status": "released",
"symbol": "KITLG",
"synonyms": [
"SF",
"WS2F",
"Kitl",
"FPH2",
"SCF",
"KL-1",
"DFNA69",
"familial progressive hyperpigmentation 2",
"mast cell growth factor",
"DCUA",
"kit ligand",
"c-Kit ligand",
"SLF",
"steel factor",
"KITLG",
"SHEP7",
"stem cell factor",
"KIT ligand",
"FPHH",
"MGF"
]
}
],
"uuid": "c8e46cd1-99ad-4fab-a87f-739905fa425e"
}