{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3215BSOP/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3215BSOP",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF4-BinE-PCR1_S41",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF4-BinE-PCR2_S47",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF4-BinE-PCR3_S137",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF4-BinE-PCR4_S143"
],
"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 [IGVFDS3215BSOP](/measurement-sets/IGVFDS3215BSOP/) 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/IGVFDS3215BSOP/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS3215BSOP](/measurement-sets/IGVFDS3215BSOP/) has sequence file(s) [IGVFFI9654OFFE](/sequence-files/IGVFFI9654OFFE/), [IGVFFI7817UFSJ](/sequence-files/IGVFFI7817UFSJ/), [IGVFFI6643VIJQ](/sequence-files/IGVFFI6643VIJQ/), [IGVFFI0294ZOLF](/sequence-files/IGVFFI0294ZOLF/) 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/IGVFDS3215BSOP/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM3377SBLH](/in-vitro-systems/IGVFSM3377SBLH/) 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/IGVFSM3377SBLH/"
},
{
"category": "missing publication",
"detail": "Auxiliary set [IGVFDS4590CBRM](/auxiliary-sets/IGVFDS4590CBRM/) 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/IGVFDS4590CBRM/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM3377SBLH](/in-vitro-systems/IGVFSM3377SBLH/) 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/IGVFSM3377SBLH/"
}
]
},
"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": "2024-05-16T17:33:46.577731+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/IGVFFI1543ISBB/",
"accession": "IGVFFI1543ISBB",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF4-BinE-PCR3_S137"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:08:59.111647+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI1543ISBB/@@download/IGVFFI1543ISBB.yaml.gz",
"md5sum": "8d4abf797fb1672553cc341d43af2f30",
"s3_uri": "s3://igvf-files/2024/06/11/0d68419b-ada5-452f-91d9-f1c96254f930/IGVFFI1543ISBB.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF4-BinE-PCR3_S137.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI9076ESKZ/",
"accession": "IGVFFI9076ESKZ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF4-BinE-PCR1_S41"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:08:30.992087+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI9076ESKZ/@@download/IGVFFI9076ESKZ.yaml.gz",
"md5sum": "df0fbede16aede0bf62b1bae44e64e2e",
"s3_uri": "s3://igvf-files/2024/06/11/91635fe9-7304-42c0-9e38-3d8f31d45bba/IGVFFI9076ESKZ.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF4-BinE-PCR1_S41.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI1298TKBV/",
"accession": "IGVFFI1298TKBV",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF4-BinE-PCR4_S143"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:09:13.633917+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI1298TKBV/@@download/IGVFFI1298TKBV.yaml.gz",
"md5sum": "c03d850d793155c166f6c0ffb9454597",
"s3_uri": "s3://igvf-files/2024/06/11/ea89ce78-786c-4299-8004-3920d465af4f/IGVFFI1298TKBV.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF4-BinE-PCR4_S143.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI7790ILMG/",
"accession": "IGVFFI7790ILMG",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF4-BinE-PCR2_S47"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:08:44.789169+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI7790ILMG/@@download/IGVFFI7790ILMG.yaml.gz",
"md5sum": "edfa21512e7d2071af09b71becf83cb8",
"s3_uri": "s3://igvf-files/2024/06/11/c334cbe1-d01c-471c-baa7-7affccc8448c/IGVFFI7790ILMG.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF4-BinE-PCR2_S47.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI9654OFFE/",
"accession": "IGVFFI9654OFFE",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF4-BinE-PCR2_S47"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:19:12.571485+00:00",
"file_format": "fastq",
"file_size": 6769660,
"href": "/sequence-files/IGVFFI9654OFFE/@@download/IGVFFI9654OFFE.fastq.gz",
"md5sum": "f65faa78fee59dabd26142c848bb2da7",
"s3_uri": "s3://igvf-files/2024/06/01/95771f19-b6e4-459f-b907-b4a4991b5fad/IGVFFI9654OFFE.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-BinE-PCR2_S47_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7817UFSJ/",
"accession": "IGVFFI7817UFSJ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF4-BinE-PCR4_S143"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:19:48.827747+00:00",
"file_format": "fastq",
"file_size": 15082646,
"href": "/sequence-files/IGVFFI7817UFSJ/@@download/IGVFFI7817UFSJ.fastq.gz",
"md5sum": "85a20d82ccb6d41f8ca493ba83ad27f0",
"s3_uri": "s3://igvf-files/2024/06/01/62a0fcdf-842e-4923-aea2-798391c45343/IGVFFI7817UFSJ.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-BinE-PCR4_S143_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6643VIJQ/",
"accession": "IGVFFI6643VIJQ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF4-BinE-PCR3_S137"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:19:30.478027+00:00",
"file_format": "fastq",
"file_size": 15894366,
"href": "/sequence-files/IGVFFI6643VIJQ/@@download/IGVFFI6643VIJQ.fastq.gz",
"md5sum": "4ea9e019d79c647f200164e6fe7d9632",
"s3_uri": "s3://igvf-files/2024/06/01/7247bc29-b627-48bb-8c76-c9ad99520c76/IGVFFI6643VIJQ.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-BinE-PCR3_S137_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0294ZOLF/",
"accession": "IGVFFI0294ZOLF",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF4-BinE-PCR1_S41"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:18:53.073476+00:00",
"file_format": "fastq",
"file_size": 9518768,
"href": "/sequence-files/IGVFFI0294ZOLF/@@download/IGVFFI0294ZOLF.fastq.gz",
"md5sum": "82dc8dfb8270397ce7731f8c00048f38",
"s3_uri": "s3://igvf-files/2024/06/01/e1a76f3e-fa75-4cff-b08c-ffc077e5d5ee/IGVFFI0294ZOLF.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-BinE-PCR1_S41_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": "2024-07-10T19:43:54.584258+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3377SBLH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3377SBLH",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinE-PCR1_S41",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinE-PCR2_S47",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinE-PCR3_S137",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinE-PCR4_S143"
],
"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 E for 80-90% 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": "2024-06-01T02:18:53.073476+00:00",
"summary": " 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": "d82f7d20-1ff2-4316-94b1-67e1d25ae455"
}