{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1505VYUV/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1505VYUV",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR1_S49",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR2_S55",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR3_S145",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR4_S151"
],
"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 [IGVFDS1505VYUV](/measurement-sets/IGVFDS1505VYUV/) 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/IGVFDS1505VYUV/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS1505VYUV](/measurement-sets/IGVFDS1505VYUV/) has sequence file(s) [IGVFFI9315VFMT](/sequence-files/IGVFFI9315VFMT/), [IGVFFI2101KHOH](/sequence-files/IGVFFI2101KHOH/), [IGVFFI6411ZRDE](/sequence-files/IGVFFI6411ZRDE/), [IGVFFI8335UTTJ](/sequence-files/IGVFFI8335UTTJ/) 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/IGVFDS1505VYUV/"
},
{
"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 [IGVFSM6859FEHH](/in-vitro-systems/IGVFSM6859FEHH/) 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/IGVFSM6859FEHH/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM6859FEHH](/in-vitro-systems/IGVFSM6859FEHH/) 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/IGVFSM6859FEHH/"
}
]
},
"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": "2024-05-16T17:56:24.727712+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/IGVFFI1495XMKJ/",
"accession": "IGVFFI1495XMKJ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR2_S55"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:09:33.858069+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI1495XMKJ/@@download/IGVFFI1495XMKJ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/b83b3244-af65-4059-bf1f-1270ea8d3ba4/IGVFFI1495XMKJ.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF1-BinA-PCR2_S55.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI1838QYEH/",
"accession": "IGVFFI1838QYEH",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR3_S145"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:09:48.811023+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI1838QYEH/@@download/IGVFFI1838QYEH.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/f6a9caec-7bb3-441a-a27d-706009db62d6/IGVFFI1838QYEH.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF1-BinA-PCR3_S145.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI9315VFMT/",
"accession": "IGVFFI9315VFMT",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR3_S145"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:20:37.436735+00:00",
"file_format": "fastq",
"file_size": 25312994,
"href": "/sequence-files/IGVFFI9315VFMT/@@download/IGVFFI9315VFMT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/553b5cd2-e3d5-4615-a5e6-c3160b9e2113/IGVFFI9315VFMT.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-BinA-PCR3_S145_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2519BAOP/",
"accession": "IGVFFI2519BAOP",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR4_S151"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:10:03.708778+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI2519BAOP/@@download/IGVFFI2519BAOP.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/f2948797-08ea-4bda-86d7-ce0265e556a4/IGVFFI2519BAOP.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF1-BinA-PCR4_S151.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI0901ITUC/",
"accession": "IGVFFI0901ITUC",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR1_S49"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:09:18.336327+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI0901ITUC/@@download/IGVFFI0901ITUC.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/05c50283-db8e-4fa1-b123-1499d2fc2dbb/IGVFFI0901ITUC.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF1-BinA-PCR1_S49.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI2101KHOH/",
"accession": "IGVFFI2101KHOH",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR2_S55"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:20:16.661412+00:00",
"file_format": "fastq",
"file_size": 7121098,
"href": "/sequence-files/IGVFFI2101KHOH/@@download/IGVFFI2101KHOH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/bcd1b250-72c0-4803-a923-974b92d2ce81/IGVFFI2101KHOH.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-BinA-PCR2_S55_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6411ZRDE/",
"accession": "IGVFFI6411ZRDE",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR1_S49"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:19:56.748397+00:00",
"file_format": "fastq",
"file_size": 11164702,
"href": "/sequence-files/IGVFFI6411ZRDE/@@download/IGVFFI6411ZRDE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/058fb837-83b6-4c6f-aa8b-59241add2d18/IGVFFI6411ZRDE.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-BinA-PCR1_S49_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8335UTTJ/",
"accession": "IGVFFI8335UTTJ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR4_S151"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:20:55.444582+00:00",
"file_format": "fastq",
"file_size": 19453121,
"href": "/sequence-files/IGVFFI8335UTTJ/@@download/IGVFFI8335UTTJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/28652d54-f5e3-4b2d-bdb1-01593b2276e9/IGVFFI8335UTTJ.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-BinA-PCR4_S151_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": "2024-07-10T19:44:05.801524+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM6859FEHH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6859FEHH",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR1_S49",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR2_S55",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR3_S145",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR4_S151"
],
"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 A for 0-10% 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": "2024-06-01T02:19:56.748397+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": "bc7ef725-bdcd-46c3-b221-4eb754c596e5"
}