{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9854LKEK/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9854LKEK",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF1-BinE-PCR4_S155",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF1-BinE-PCR1_S53",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF1-BinE-PCR2_S59",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF1-BinE-PCR3_S149"
],
"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 [IGVFDS9854LKEK](/measurement-sets/IGVFDS9854LKEK/) 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/IGVFDS9854LKEK/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS9854LKEK](/measurement-sets/IGVFDS9854LKEK/) has sequence file(s) [IGVFFI5495BLZU](/sequence-files/IGVFFI5495BLZU/), [IGVFFI8095OZBO](/sequence-files/IGVFFI8095OZBO/), [IGVFFI7074AAJO](/sequence-files/IGVFFI7074AAJO/), [IGVFFI8313IJZX](/sequence-files/IGVFFI8313IJZX/) 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/IGVFDS9854LKEK/"
},
{
"category": "missing publication",
"detail": "Auxiliary set [IGVFDS4521OAKZ](/auxiliary-sets/IGVFDS4521OAKZ/) 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/IGVFDS4521OAKZ/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM7459KLMD](/in-vitro-systems/IGVFSM7459KLMD/) 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/IGVFSM7459KLMD/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM7459KLMD](/in-vitro-systems/IGVFSM7459KLMD/) 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/IGVFSM7459KLMD/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS4521OAKZ/",
"accession": "IGVFDS4521OAKZ",
"aliases": [
"jesse-engreitz:auxiliary_sortparams_CRUDO_KITLG-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/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": "2024-05-16T17:56:30.218281+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/IGVFFI9139DGUG/",
"accession": "IGVFFI9139DGUG",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF1-BinE-PCR4_S155"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:10:13.512032+00:00",
"file_format": "yaml",
"file_size": 905,
"href": "/configuration-files/IGVFFI9139DGUG/@@download/IGVFFI9139DGUG.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/a02a7601-5a30-4428-9a05-1833ec1dab39/IGVFFI9139DGUG.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF1-BinE-PCR4_S155.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI5495BLZU/",
"accession": "IGVFFI5495BLZU",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF1-BinE-PCR4_S155"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T15:21:58.204038+00:00",
"file_format": "fastq",
"file_size": 18566372,
"href": "/sequence-files/IGVFFI5495BLZU/@@download/IGVFFI5495BLZU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/e7c900c3-b510-4daa-98c2-05d2d89806cc/IGVFFI5495BLZU.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/Auxin6hrs-FF1-BinE-PCR4_S155_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5367BEYQ/",
"accession": "IGVFFI5367BEYQ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF1-BinE-PCR2_S59"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:09:43.648525+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI5367BEYQ/@@download/IGVFFI5367BEYQ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/2a2afa51-c728-4750-856d-183c5a60e192/IGVFFI5367BEYQ.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF1-BinE-PCR2_S59.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI7915FWLA/",
"accession": "IGVFFI7915FWLA",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF1-BinE-PCR1_S53"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:09:28.994936+00:00",
"file_format": "yaml",
"file_size": 900,
"href": "/configuration-files/IGVFFI7915FWLA/@@download/IGVFFI7915FWLA.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/8edea630-65e7-447f-9ac2-cc6e2a0c267e/IGVFFI7915FWLA.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF1-BinE-PCR1_S53.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI4427FAAQ/",
"accession": "IGVFFI4427FAAQ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF1-BinE-PCR3_S149"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:09:58.704511+00:00",
"file_format": "yaml",
"file_size": 904,
"href": "/configuration-files/IGVFFI4427FAAQ/@@download/IGVFFI4427FAAQ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/06d26e51-9d1b-43cb-9ebb-2f13bbcbc024/IGVFFI4427FAAQ.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF1-BinE-PCR3_S149.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI8095OZBO/",
"accession": "IGVFFI8095OZBO",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF1-BinE-PCR2_S59"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:20:31.432512+00:00",
"file_format": "fastq",
"file_size": 13685404,
"href": "/sequence-files/IGVFFI8095OZBO/@@download/IGVFFI8095OZBO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/9dc8d6c3-e8b0-4d8e-aeaa-85d031c6715c/IGVFFI8095OZBO.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/Auxin6hrs-FF1-BinE-PCR2_S59_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7074AAJO/",
"accession": "IGVFFI7074AAJO",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF1-BinE-PCR1_S53"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:20:10.738183+00:00",
"file_format": "fastq",
"file_size": 8479992,
"href": "/sequence-files/IGVFFI7074AAJO/@@download/IGVFFI7074AAJO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/30390d62-c052-494b-bc15-b17c5da83e2e/IGVFFI7074AAJO.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/Auxin6hrs-FF1-BinE-PCR1_S53_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8313IJZX/",
"accession": "IGVFFI8313IJZX",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF1-BinE-PCR3_S149"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:20:49.468295+00:00",
"file_format": "fastq",
"file_size": 17166135,
"href": "/sequence-files/IGVFFI8313IJZX/@@download/IGVFFI8313IJZX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/92bdc5ee-633c-4e12-a365-f77ab66c9cc8/IGVFFI8313IJZX.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/Auxin6hrs-FF1-BinE-PCR3_S149_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. The original alias jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF1-BinD-PCR4_S155 was changed to jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF1-BinE-PCR4_S155",
"preferred_assay_title": "CRISPR FlowFISH screen",
"protocols": [
"https://www.protocols.io/view/crispri-of-regulatory-elements-upon-degron-operati-5jyl82d59l2w/v1"
],
"release_timestamp": "2024-07-10T19:44:26.927985+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7459KLMD/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7459KLMD",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF1-BinE-PCR4_S155",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF1-BinE-PCR1_S53",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF1-BinE-PCR2_S59",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF1-BinE-PCR3_S149"
],
"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 E for 80-90% expression of KITLG) 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": "2024-06-01T02:20:10.738183+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": "403bed6f-94b8-4f3c-96c9-37213b6702bb"
}