{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5041NPBP/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5041NPBP",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF4-BinF-PCR1_S42",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF4-BinF-PCR2_S48",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF4-BinF-PCR3_S138",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF4-BinF-PCR4_S144"
],
"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 sequencing kit",
"detail": "Measurement set [IGVFDS5041NPBP](/measurement-sets/IGVFDS5041NPBP/) has sequence file(s) [IGVFFI7703FLHW](/sequence-files/IGVFFI7703FLHW/), [IGVFFI1945MHRX](/sequence-files/IGVFFI1945MHRX/), [IGVFFI2786CBJE](/sequence-files/IGVFFI2786CBJE/), [IGVFFI6557KAII](/sequence-files/IGVFFI6557KAII/) 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/IGVFDS5041NPBP/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM1131LTFK](/in-vitro-systems/IGVFSM1131LTFK/) 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/IGVFSM1131LTFK/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS4590CBRM/",
"accession": "IGVFDS4590CBRM",
"aliases": [
"jesse-engreitz:auxiliary_sortparams_CRUDO_KITLG-Auxin0hrs-FF4"
],
"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": "2024-05-16T17:33:47.521629+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/IGVFFI2418FKKK/",
"accession": "IGVFFI2418FKKK",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF4-BinF-PCR3_S138"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:09:01.513661+00:00",
"file_format": "yaml",
"file_size": 904,
"href": "/configuration-files/IGVFFI2418FKKK/@@download/IGVFFI2418FKKK.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/f3b0be57-c5c1-42fc-8b1a-fb7dd7873c43/IGVFFI2418FKKK.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF4-BinF-PCR3_S138.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI9623WQKP/",
"accession": "IGVFFI9623WQKP",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF4-BinF-PCR4_S144"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:09:16.017288+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI9623WQKP/@@download/IGVFFI9623WQKP.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/804a8ae9-8b35-4316-a599-a34eb8d75769/IGVFFI9623WQKP.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF4-BinF-PCR4_S144.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI7142EQVW/",
"accession": "IGVFFI7142EQVW",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF4-BinF-PCR2_S48"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:08:47.140772+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI7142EQVW/@@download/IGVFFI7142EQVW.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/f251631a-e414-4884-b565-efce814984ea/IGVFFI7142EQVW.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF4-BinF-PCR2_S48.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI9051FMRX/",
"accession": "IGVFFI9051FMRX",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF4-BinF-PCR1_S42"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:08:33.163423+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI9051FMRX/@@download/IGVFFI9051FMRX.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/44c59408-f2b7-46d0-a859-f6f157057539/IGVFFI9051FMRX.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF4-BinF-PCR1_S42.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI7703FLHW/",
"accession": "IGVFFI7703FLHW",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF4-BinF-PCR4_S144"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:19:53.630489+00:00",
"file_format": "fastq",
"file_size": 19854914,
"href": "/sequence-files/IGVFFI7703FLHW/@@download/IGVFFI7703FLHW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/1c3645f2-ac1c-4777-90c1-add3dbc2ff25/IGVFFI7703FLHW.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-FF4-BinF-PCR4_S144_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1945MHRX/",
"accession": "IGVFFI1945MHRX",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF4-BinF-PCR3_S138"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:19:33.505336+00:00",
"file_format": "fastq",
"file_size": 28520131,
"href": "/sequence-files/IGVFFI1945MHRX/@@download/IGVFFI1945MHRX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/b3e464d5-026c-4e10-943d-cdd3b5c91b77/IGVFFI1945MHRX.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-FF4-BinF-PCR3_S138_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2786CBJE/",
"accession": "IGVFFI2786CBJE",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF4-BinF-PCR2_S48"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:19:15.191152+00:00",
"file_format": "fastq",
"file_size": 10504766,
"href": "/sequence-files/IGVFFI2786CBJE/@@download/IGVFFI2786CBJE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/90653a57-9bcd-4c7e-afcc-97c7c2f63d90/IGVFFI2786CBJE.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-FF4-BinF-PCR2_S48_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6557KAII/",
"accession": "IGVFFI6557KAII",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF4-BinF-PCR1_S42"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:18:56.081838+00:00",
"file_format": "fastq",
"file_size": 9120671,
"href": "/sequence-files/IGVFFI6557KAII/@@download/IGVFFI6557KAII.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/137220dd-40c7-46b8-bcf2-c0d0629d3877/IGVFFI6557KAII.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-FF4-BinF-PCR1_S42_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": "2024-07-10T19:43:59.522004+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1131LTFK/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1131LTFK",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinF-PCR1_S42",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinF-PCR2_S48",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinF-PCR3_S138",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinF-PCR4_S144"
],
"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": "HCT116 cell line, male, Homo sapiens (sorting details: FACS bin F for 80-100% 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": "25",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-01T02:18:56.081838+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": [
"DFNA69",
"WS2F",
"DCUA",
"familial progressive hyperpigmentation 2",
"KL-1",
"FPHH",
"MGF",
"c-Kit ligand",
"FPH2",
"steel factor",
"SHEP7",
"mast cell growth factor",
"kit ligand",
"Kitl",
"stem cell factor",
"SLF",
"SCF",
"SF"
]
}
],
"uuid": "fe1a8271-fd7e-454e-ae2c-187f1d46d77d"
}