{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0097SVOJ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0097SVOJ",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF3-BinC-PCR1_S75",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF3-BinC-PCR2_S81",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF3-BinC-PCR3_S171",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF3-BinC-PCR4_S177"
],
"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 [IGVFDS7947IZNE](/auxiliary-sets/IGVFDS7947IZNE/) 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/IGVFDS7947IZNE/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS0097SVOJ](/measurement-sets/IGVFDS0097SVOJ/) 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/IGVFDS0097SVOJ/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS0097SVOJ](/measurement-sets/IGVFDS0097SVOJ/) has sequence file(s) [IGVFFI3322NUTZ](/sequence-files/IGVFFI3322NUTZ/), [IGVFFI7576UXRP](/sequence-files/IGVFFI7576UXRP/), [IGVFFI2587SEJV](/sequence-files/IGVFFI2587SEJV/), [IGVFFI7034TURO](/sequence-files/IGVFFI7034TURO/) 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/IGVFDS0097SVOJ/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM2991GHKL](/in-vitro-systems/IGVFSM2991GHKL/) 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/IGVFSM2991GHKL/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM2991GHKL](/in-vitro-systems/IGVFSM2991GHKL/) 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/IGVFSM2991GHKL/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS7947IZNE/",
"accession": "IGVFDS7947IZNE",
"aliases": [
"jesse-engreitz:auxiliary_sortparams_CRUDO_KITLG-Auxin6hrs-FF3"
],
"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": "2024-05-16T17:57:20.124625+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/IGVFFI9807MXMC/",
"accession": "IGVFFI9807MXMC",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF3-BinC-PCR2_S81"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:11:38.532444+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI9807MXMC/@@download/IGVFFI9807MXMC.yaml.gz",
"md5sum": "2dbe7b5e960a38a8190f5b1ed3b8e7cc",
"s3_uri": "s3://igvf-files/2024/06/11/81eb1335-065c-435d-89e6-4683907be615/IGVFFI9807MXMC.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF3-BinC-PCR2_S81.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI8268KMIE/",
"accession": "IGVFFI8268KMIE",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF3-BinC-PCR3_S171"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:11:53.502440+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI8268KMIE/@@download/IGVFFI8268KMIE.yaml.gz",
"md5sum": "45e804be7caf305f957e6c4b40546bd4",
"s3_uri": "s3://igvf-files/2024/06/11/82b76ebd-fab2-472d-8792-bdfaa7e2e37c/IGVFFI8268KMIE.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF3-BinC-PCR3_S171.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI1566RQOI/",
"accession": "IGVFFI1566RQOI",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF3-BinC-PCR4_S177"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:12:07.674427+00:00",
"file_format": "yaml",
"file_size": 904,
"href": "/configuration-files/IGVFFI1566RQOI/@@download/IGVFFI1566RQOI.yaml.gz",
"md5sum": "f5c97bb8c7fce9c1a24e422b2233eeb7",
"s3_uri": "s3://igvf-files/2024/06/11/0dbd7bbc-6b04-487a-93fe-87fe353c73dc/IGVFFI1566RQOI.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF3-BinC-PCR4_S177.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI7524POSB/",
"accession": "IGVFFI7524POSB",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF3-BinC-PCR1_S75"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:11:24.092988+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI7524POSB/@@download/IGVFFI7524POSB.yaml.gz",
"md5sum": "58dff02ebe91b85dd077b29c0ee4d635",
"s3_uri": "s3://igvf-files/2024/06/11/bd384c99-476e-42b2-a647-3fdbf3af321b/IGVFFI7524POSB.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF3-BinC-PCR1_S75.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI3322NUTZ/",
"accession": "IGVFFI3322NUTZ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF3-BinC-PCR4_S177"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T15:27:39.646625+00:00",
"file_format": "fastq",
"file_size": 20458596,
"href": "/sequence-files/IGVFFI3322NUTZ/@@download/IGVFFI3322NUTZ.fastq.gz",
"md5sum": "4148eec4bc61e49f1b961f5931802381",
"s3_uri": "s3://igvf-files/2024/06/03/83716f1c-e6d9-40dd-b44d-eb91bbf39931/IGVFFI3322NUTZ.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-FF3-BinC-PCR4_S177_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7576UXRP/",
"accession": "IGVFFI7576UXRP",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF3-BinC-PCR3_S171"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T15:27:22.584451+00:00",
"file_format": "fastq",
"file_size": 15672358,
"href": "/sequence-files/IGVFFI7576UXRP/@@download/IGVFFI7576UXRP.fastq.gz",
"md5sum": "45a9d910af0a5246e07e8b7e410e1f9f",
"s3_uri": "s3://igvf-files/2024/06/03/0a4c518f-34db-48c9-ae6e-f33b02ccd081/IGVFFI7576UXRP.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-FF3-BinC-PCR3_S171_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2587SEJV/",
"accession": "IGVFFI2587SEJV",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF3-BinC-PCR1_S75"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T15:26:50.520573+00:00",
"file_format": "fastq",
"file_size": 7265950,
"href": "/sequence-files/IGVFFI2587SEJV/@@download/IGVFFI2587SEJV.fastq.gz",
"md5sum": "6a137a924158fb90997ae409c2bd4e52",
"s3_uri": "s3://igvf-files/2024/06/03/daa8e22f-5bf9-4aac-8011-920bf1827b7e/IGVFFI2587SEJV.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-FF3-BinC-PCR1_S75_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7034TURO/",
"accession": "IGVFFI7034TURO",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF3-BinC-PCR2_S81"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T15:27:06.474900+00:00",
"file_format": "fastq",
"file_size": 7459911,
"href": "/sequence-files/IGVFFI7034TURO/@@download/IGVFFI7034TURO.fastq.gz",
"md5sum": "939371104f65457b4e813bcd24831ac0",
"s3_uri": "s3://igvf-files/2024/06/03/5817d75c-505e-41eb-8c61-d38033b7f117/IGVFFI7034TURO.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-FF3-BinC-PCR2_S81_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": "2024-07-10T19:45:20.192328+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2991GHKL/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2991GHKL",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF3-BinC-PCR1_S75",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF3-BinC-PCR2_S81",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF3-BinC-PCR3_S171",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF3-BinC-PCR4_S177"
],
"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": "2024-06-03T15:26:50.520573+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": "5266be78-2365-475d-a525-7272285ce712"
}