{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9772ARQM/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9772ARQM",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF2-BinA-PCR1_S61",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF2-BinA-PCR2_S67",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF2-BinA-PCR3_S157",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF2-BinA-PCR4_S163"
],
"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 [IGVFDS8781ZUPM](/auxiliary-sets/IGVFDS8781ZUPM/) 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/IGVFDS8781ZUPM/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM8085CGHV](/in-vitro-systems/IGVFSM8085CGHV/) 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/IGVFSM8085CGHV/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS9772ARQM](/measurement-sets/IGVFDS9772ARQM/) 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/IGVFDS9772ARQM/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS9772ARQM](/measurement-sets/IGVFDS9772ARQM/) has sequence file(s) [IGVFFI0997LMOA](/sequence-files/IGVFFI0997LMOA/), [IGVFFI7283SWVN](/sequence-files/IGVFFI7283SWVN/), [IGVFFI4625BMCS](/sequence-files/IGVFFI4625BMCS/), [IGVFFI4782QJVA](/sequence-files/IGVFFI4782QJVA/) 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/IGVFDS9772ARQM/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM8085CGHV](/in-vitro-systems/IGVFSM8085CGHV/) 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/IGVFSM8085CGHV/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS8781ZUPM/",
"accession": "IGVFDS8781ZUPM",
"aliases": [
"jesse-engreitz:auxiliary_sortparams_CRUDO_KITLG-Auxin6hrs-FF2"
],
"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": "2024-05-16T17:56:52.192206+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/IGVFFI0920UKZB/",
"accession": "IGVFFI0920UKZB",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF2-BinA-PCR4_S163"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:11:05.013184+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI0920UKZB/@@download/IGVFFI0920UKZB.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/1b0f36bb-e24d-4c15-a2b0-16deca0c9d05/IGVFFI0920UKZB.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF2-BinA-PCR4_S163.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI3220MAND/",
"accession": "IGVFFI3220MAND",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF2-BinA-PCR2_S67"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:10:33.236478+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI3220MAND/@@download/IGVFFI3220MAND.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/28a21c49-e3ed-4ff8-85b6-c9d5d204c608/IGVFFI3220MAND.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF2-BinA-PCR2_S67.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI0997LMOA/",
"accession": "IGVFFI0997LMOA",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF2-BinA-PCR2_S67"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T15:22:43.030974+00:00",
"file_format": "fastq",
"file_size": 9029343,
"href": "/sequence-files/IGVFFI0997LMOA/@@download/IGVFFI0997LMOA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/ce9d94eb-afce-48a4-962d-e4fbef46fe4c/IGVFFI0997LMOA.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-FF2-BinA-PCR2_S67_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0959LGYD/",
"accession": "IGVFFI0959LGYD",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF2-BinA-PCR1_S61"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:10:18.188771+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI0959LGYD/@@download/IGVFFI0959LGYD.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/46c97bf5-4654-41a9-950f-43680b706ab1/IGVFFI0959LGYD.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF2-BinA-PCR1_S61.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI8082BFNJ/",
"accession": "IGVFFI8082BFNJ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF2-BinA-PCR3_S157"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:10:48.053295+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI8082BFNJ/@@download/IGVFFI8082BFNJ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/87765a47-21c4-4605-8dc6-4f7920474b04/IGVFFI8082BFNJ.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF2-BinA-PCR3_S157.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI7283SWVN/",
"accession": "IGVFFI7283SWVN",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF2-BinA-PCR4_S163"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T15:26:27.375980+00:00",
"file_format": "fastq",
"file_size": 18618625,
"href": "/sequence-files/IGVFFI7283SWVN/@@download/IGVFFI7283SWVN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/71d4c38d-50ea-49aa-b68a-9fd20beaf7d5/IGVFFI7283SWVN.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-FF2-BinA-PCR4_S163_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4625BMCS/",
"accession": "IGVFFI4625BMCS",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF2-BinA-PCR3_S157"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T15:26:06.444502+00:00",
"file_format": "fastq",
"file_size": 40971037,
"href": "/sequence-files/IGVFFI4625BMCS/@@download/IGVFFI4625BMCS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/bb9bbd01-2aa1-4873-9ba4-bfff433c072d/IGVFFI4625BMCS.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-FF2-BinA-PCR3_S157_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4782QJVA/",
"accession": "IGVFFI4782QJVA",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF2-BinA-PCR1_S61"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T15:22:25.922961+00:00",
"file_format": "fastq",
"file_size": 22242207,
"href": "/sequence-files/IGVFFI4782QJVA/@@download/IGVFFI4782QJVA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/6e614558-f9fb-4fd6-8e98-fa8947e993b0/IGVFFI4782QJVA.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-FF2-BinA-PCR1_S61_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS6482AXWW/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"notes": "This dataset originally had the alias jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF2-BinB-PCR3_S157 but it was changed to jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF2-BinA-PCR3_S157.",
"preferred_assay_title": "CRISPR FlowFISH screen",
"protocols": [
"https://www.protocols.io/view/crispri-of-regulatory-elements-upon-degron-operati-5jyl82d59l2w/v1"
],
"release_timestamp": "2024-07-10T19:44:37.347679+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8085CGHV/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8085CGHV",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF2-BinA-PCR1_S61",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF2-BinA-PCR2_S67",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF2-BinA-PCR3_S157",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF2-BinA-PCR4_S163"
],
"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": "2024-06-03T15:22:25.922961+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": "4434352e-690d-4d33-87ea-069291465d48"
}