{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4623YYCA/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4623YYCA",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinF-PCR1_S18",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinF-PCR2_S24",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinF-PCR3_S114",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinF-PCR4_S120"
],
"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 [IGVFDS4623YYCA](/measurement-sets/IGVFDS4623YYCA/) 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/IGVFDS4623YYCA/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS4623YYCA](/measurement-sets/IGVFDS4623YYCA/) has sequence file(s) [IGVFFI5488NRJE](/sequence-files/IGVFFI5488NRJE/), [IGVFFI4644CRZB](/sequence-files/IGVFFI4644CRZB/), [IGVFFI4200EWKJ](/sequence-files/IGVFFI4200EWKJ/), [IGVFFI3207TTVR](/sequence-files/IGVFFI3207TTVR/) 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/IGVFDS4623YYCA/"
},
{
"category": "missing publication",
"detail": "Auxiliary set [IGVFDS4522DABT](/auxiliary-sets/IGVFDS4522DABT/) 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/IGVFDS4522DABT/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM1737WNTH](/in-vitro-systems/IGVFSM1737WNTH/) 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/IGVFSM1737WNTH/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM1737WNTH](/in-vitro-systems/IGVFSM1737WNTH/) 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/IGVFSM1737WNTH/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS4522DABT/",
"accession": "IGVFDS4522DABT",
"aliases": [
"jesse-engreitz:auxiliary_sortparams_CRUDO_KITLG-Auxin0hrs-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": "2024-05-16T17:33:01.113165+00:00",
"data_use_limitation_summaries": [
"no certificate"
],
"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/IGVFFI9179ZFTQ/",
"accession": "IGVFFI9179ZFTQ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF2-BinF-PCR3_S114"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:07:13.393591+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI9179ZFTQ/@@download/IGVFFI9179ZFTQ.yaml.gz",
"md5sum": "f69f82e9606ce55f5c79d1d592fc109a",
"s3_uri": "s3://igvf-files/2024/06/11/30a3219f-86d1-4f63-86df-542f7ec19925/IGVFFI9179ZFTQ.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF2-BinF-PCR3_S114.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI1929STRW/",
"accession": "IGVFFI1929STRW",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF2-BinF-PCR1_S18"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:06:46.414136+00:00",
"file_format": "yaml",
"file_size": 900,
"href": "/configuration-files/IGVFFI1929STRW/@@download/IGVFFI1929STRW.yaml.gz",
"md5sum": "ac47e24efb94715fe82eb2690b520931",
"s3_uri": "s3://igvf-files/2024/06/11/4f759968-432a-4482-b9b1-145e91ce4991/IGVFFI1929STRW.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF2-BinF-PCR1_S18.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI4146MVTA/",
"accession": "IGVFFI4146MVTA",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF2-BinF-PCR4_S120"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:07:26.708785+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI4146MVTA/@@download/IGVFFI4146MVTA.yaml.gz",
"md5sum": "2782ec01ead4aac17d917724ebc527bd",
"s3_uri": "s3://igvf-files/2024/06/11/147ad493-d576-4142-b6f1-bf6ff52ddc43/IGVFFI4146MVTA.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF2-BinF-PCR4_S120.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI4786CMQR/",
"accession": "IGVFFI4786CMQR",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF2-BinF-PCR2_S24"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:06:59.996074+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI4786CMQR/@@download/IGVFFI4786CMQR.yaml.gz",
"md5sum": "5fc967aa1441540442308403ff324c7f",
"s3_uri": "s3://igvf-files/2024/06/11/2214d1e5-d296-4952-93f1-5f64aaa282d6/IGVFFI4786CMQR.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF2-BinF-PCR2_S24.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI5488NRJE/",
"accession": "IGVFFI5488NRJE",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF2-BinF-PCR2_S24"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:15:02.033147+00:00",
"file_format": "fastq",
"file_size": 15233292,
"href": "/sequence-files/IGVFFI5488NRJE/@@download/IGVFFI5488NRJE.fastq.gz",
"md5sum": "76700ace6bf719b75ea0bd364ba1bf8b",
"s3_uri": "s3://igvf-files/2024/06/01/26beaf4b-b9bb-459b-ab6c-bc1bad3994cb/IGVFFI5488NRJE.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-FF2-BinF-PCR2_S24_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4644CRZB/",
"accession": "IGVFFI4644CRZB",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF2-BinF-PCR3_S114"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:17:04.257822+00:00",
"file_format": "fastq",
"file_size": 22488401,
"href": "/sequence-files/IGVFFI4644CRZB/@@download/IGVFFI4644CRZB.fastq.gz",
"md5sum": "934a976456e3f74f5f5752b6857f2830",
"s3_uri": "s3://igvf-files/2024/06/01/158fd8ac-6a3d-4bb3-8649-9dc6a961094e/IGVFFI4644CRZB.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-FF2-BinF-PCR3_S114_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4200EWKJ/",
"accession": "IGVFFI4200EWKJ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF2-BinF-PCR4_S120"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:17:22.028765+00:00",
"file_format": "fastq",
"file_size": 30569605,
"href": "/sequence-files/IGVFFI4200EWKJ/@@download/IGVFFI4200EWKJ.fastq.gz",
"md5sum": "42c85265c016f79dce86945dc9630c38",
"s3_uri": "s3://igvf-files/2024/06/01/db5f83ec-218f-436b-8528-fb9a4f1b32dc/IGVFFI4200EWKJ.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-FF2-BinF-PCR4_S120_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3207TTVR/",
"accession": "IGVFFI3207TTVR",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF2-BinF-PCR1_S18"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:14:44.348505+00:00",
"file_format": "fastq",
"file_size": 11348763,
"href": "/sequence-files/IGVFFI3207TTVR/@@download/IGVFFI3207TTVR.fastq.gz",
"md5sum": "cf9079a4bd8b6e91c6dec84149f26f3c",
"s3_uri": "s3://igvf-files/2024/06/01/f3426c18-3772-445d-9f19-4c263f1190d4/IGVFFI3207TTVR.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-FF2-BinF-PCR1_S18_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": "2024-07-10T19:42:55.885602+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1737WNTH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1737WNTH",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinF-PCR1_S18",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinF-PCR2_S24",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinF-PCR3_S114",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinF-PCR4_S120"
],
"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 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": "26",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-01T02:14:44.348505+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": "73b5c3b9-ec87-42ed-9c5e-f5282b0823d8"
}