{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0360KHPL/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0360KHPL",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF4-BinC-PCR1_S87",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF4-BinC-PCR2_S93",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF4-BinC-PCR3_S183",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF4-BinC-PCR4_S189"
],
"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 [IGVFDS0877LMZO](/auxiliary-sets/IGVFDS0877LMZO/) 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/IGVFDS0877LMZO/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS0360KHPL](/measurement-sets/IGVFDS0360KHPL/) 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/IGVFDS0360KHPL/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS0360KHPL](/measurement-sets/IGVFDS0360KHPL/) has sequence file(s) [IGVFFI5521JTXL](/sequence-files/IGVFFI5521JTXL/), [IGVFFI2065WSYF](/sequence-files/IGVFFI2065WSYF/), [IGVFFI8374AEMS](/sequence-files/IGVFFI8374AEMS/), [IGVFFI4285CCHK](/sequence-files/IGVFFI4285CCHK/) 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/IGVFDS0360KHPL/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM7739FHWE](/in-vitro-systems/IGVFSM7739FHWE/) 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/IGVFSM7739FHWE/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM7739FHWE](/in-vitro-systems/IGVFSM7739FHWE/) 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/IGVFSM7739FHWE/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS0877LMZO/",
"accession": "IGVFDS0877LMZO",
"aliases": [
"jesse-engreitz:auxiliary_sortparams_CRUDO_KITLG-Auxin6hrs-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": "2024-05-16T17:57:43.457525+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/IGVFFI2881HWLY/",
"accession": "IGVFFI2881HWLY",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF4-BinC-PCR1_S87"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:12:21.901121+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI2881HWLY/@@download/IGVFFI2881HWLY.yaml.gz",
"md5sum": "a4ff0ac21c5a4f1d21cc1d4f5c50509d",
"s3_uri": "s3://igvf-files/2024/06/11/bead906b-7e73-49ae-8d57-66d797a76439/IGVFFI2881HWLY.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF4-BinC-PCR1_S87.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI1481CPMA/",
"accession": "IGVFFI1481CPMA",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF4-BinC-PCR4_S189"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:13:05.903003+00:00",
"file_format": "yaml",
"file_size": 904,
"href": "/configuration-files/IGVFFI1481CPMA/@@download/IGVFFI1481CPMA.yaml.gz",
"md5sum": "775321c44f3ec1f699d110b958a50e60",
"s3_uri": "s3://igvf-files/2024/06/11/6820bd03-7cd8-4968-998e-bfddf81b7518/IGVFFI1481CPMA.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF4-BinC-PCR4_S189.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI0861YUMY/",
"accession": "IGVFFI0861YUMY",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF4-BinC-PCR2_S93"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:12:36.519906+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI0861YUMY/@@download/IGVFFI0861YUMY.yaml.gz",
"md5sum": "b45ef5bc4b13270d7a8d5634e0a40145",
"s3_uri": "s3://igvf-files/2024/06/11/93fed33e-e63d-4d29-bf94-384449cd4883/IGVFFI0861YUMY.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF4-BinC-PCR2_S93.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI5521JTXL/",
"accession": "IGVFFI5521JTXL",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF4-BinC-PCR3_S183"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T15:28:28.987250+00:00",
"file_format": "fastq",
"file_size": 13306864,
"href": "/sequence-files/IGVFFI5521JTXL/@@download/IGVFFI5521JTXL.fastq.gz",
"md5sum": "930629d4f3e3ad7fd0196dfd134702ac",
"s3_uri": "s3://igvf-files/2024/06/03/be2daa09-7de5-4ac4-ba17-b75a31dedfbc/IGVFFI5521JTXL.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-FF4-BinC-PCR3_S183_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9429EELR/",
"accession": "IGVFFI9429EELR",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF4-BinC-PCR3_S183"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:12:51.231676+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI9429EELR/@@download/IGVFFI9429EELR.yaml.gz",
"md5sum": "0617915e74b534067d6c6832788a7ad8",
"s3_uri": "s3://igvf-files/2024/06/11/ce5c28fa-b06e-4530-8d6e-3fb002833f3f/IGVFFI9429EELR.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF4-BinC-PCR3_S183.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI2065WSYF/",
"accession": "IGVFFI2065WSYF",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF4-BinC-PCR4_S189"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T15:28:45.407230+00:00",
"file_format": "fastq",
"file_size": 11175898,
"href": "/sequence-files/IGVFFI2065WSYF/@@download/IGVFFI2065WSYF.fastq.gz",
"md5sum": "a0439f7dbd00455239378e14cd7f1525",
"s3_uri": "s3://igvf-files/2024/06/03/924e15f9-ca81-4bf7-9cf7-282bc22008e2/IGVFFI2065WSYF.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-FF4-BinC-PCR4_S189_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8374AEMS/",
"accession": "IGVFFI8374AEMS",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF4-BinC-PCR2_S93"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T15:28:12.613341+00:00",
"file_format": "fastq",
"file_size": 5005733,
"href": "/sequence-files/IGVFFI8374AEMS/@@download/IGVFFI8374AEMS.fastq.gz",
"md5sum": "2587cc4410b89f67e5d5d3ba8a9abc69",
"s3_uri": "s3://igvf-files/2024/06/03/879f25c4-e69f-4b0b-b3ed-6308c7daccbe/IGVFFI8374AEMS.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-FF4-BinC-PCR2_S93_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4285CCHK/",
"accession": "IGVFFI4285CCHK",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF4-BinC-PCR1_S87"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T15:27:56.504553+00:00",
"file_format": "fastq",
"file_size": 5489268,
"href": "/sequence-files/IGVFFI4285CCHK/@@download/IGVFFI4285CCHK.fastq.gz",
"md5sum": "394fb727ff58bc1a9d8118d7027b75f5",
"s3_uri": "s3://igvf-files/2024/06/03/6eccaf1b-f19b-4e9a-b11b-9213b337a44e/IGVFFI4285CCHK.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-FF4-BinC-PCR1_S87_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": "2024-07-10T19:45:53.947926+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7739FHWE/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7739FHWE",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF4-BinC-PCR1_S87",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF4-BinC-PCR2_S93",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF4-BinC-PCR3_S183",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF4-BinC-PCR4_S189"
],
"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 C for 35-45% 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_term_name": "5-Phenyl-1H-indole-3-acetic acid",
"treatment_type": "chemical"
}
]
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-03T15:27:56.504553+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": "25ddfad1-1530-4c44-9e2d-2b134838d1ee"
}