{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7144EOAW/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7144EOAW",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF3-BinE-PCR1_S77",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF3-BinE-PCR2_S83",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF3-BinE-PCR3_S173",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF3-BinE-PCR4_S179"
],
"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": "In vitro system [IGVFSM9250VIBU](/in-vitro-systems/IGVFSM9250VIBU/) 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/IGVFSM9250VIBU/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS7144EOAW](/measurement-sets/IGVFDS7144EOAW/) 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/IGVFDS7144EOAW/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS7144EOAW](/measurement-sets/IGVFDS7144EOAW/) has sequence file(s) [IGVFFI9918BQUQ](/sequence-files/IGVFFI9918BQUQ/), [IGVFFI6354LMIX](/sequence-files/IGVFFI6354LMIX/), [IGVFFI9827KBGQ](/sequence-files/IGVFFI9827KBGQ/), [IGVFFI4320HANL](/sequence-files/IGVFFI4320HANL/) 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/IGVFDS7144EOAW/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM9250VIBU](/in-vitro-systems/IGVFSM9250VIBU/) 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/IGVFSM9250VIBU/"
}
]
},
"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": "2024-05-16T17:57:21.930854+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/IGVFFI9098MLHI/",
"accession": "IGVFFI9098MLHI",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF3-BinE-PCR3_S173"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:11:58.133259+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI9098MLHI/@@download/IGVFFI9098MLHI.yaml.gz",
"md5sum": "14da6edf54ea1a8fc49a772974235ca5",
"s3_uri": "s3://igvf-files/2024/06/11/2aff46d0-5948-47e7-bec0-7f810e77d366/IGVFFI9098MLHI.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF3-BinE-PCR3_S173.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI0259TKVR/",
"accession": "IGVFFI0259TKVR",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF3-BinE-PCR1_S77"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:11:28.780048+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI0259TKVR/@@download/IGVFFI0259TKVR.yaml.gz",
"md5sum": "cc2808ffb28aad97068ae9b9fb197f68",
"s3_uri": "s3://igvf-files/2024/06/11/a84b41f0-c994-4845-8c72-77c9366852c0/IGVFFI0259TKVR.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF3-BinE-PCR1_S77.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI7928ULEY/",
"accession": "IGVFFI7928ULEY",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF3-BinE-PCR2_S83"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:11:43.489624+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI7928ULEY/@@download/IGVFFI7928ULEY.yaml.gz",
"md5sum": "71829dd4b9303b6e15a4cd863aaae581",
"s3_uri": "s3://igvf-files/2024/06/11/5301270b-48a0-4162-b151-fb7318280885/IGVFFI7928ULEY.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF3-BinE-PCR2_S83.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI0145JLIN/",
"accession": "IGVFFI0145JLIN",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF3-BinE-PCR4_S179"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:12:12.495176+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI0145JLIN/@@download/IGVFFI0145JLIN.yaml.gz",
"md5sum": "e30233cc891a8d42c5233bd68c5f2d40",
"s3_uri": "s3://igvf-files/2024/06/11/0e432e4c-d0f7-48a0-931f-7b9b5a6dcc2d/IGVFFI0145JLIN.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF3-BinE-PCR4_S179.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI9918BQUQ/",
"accession": "IGVFFI9918BQUQ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF3-BinE-PCR1_S77"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T15:26:56.063680+00:00",
"file_format": "fastq",
"file_size": 5744192,
"href": "/sequence-files/IGVFFI9918BQUQ/@@download/IGVFFI9918BQUQ.fastq.gz",
"md5sum": "ce3e7b7830eb08bbb2725b190c1767f1",
"s3_uri": "s3://igvf-files/2024/06/03/c2c1e456-2e8f-4c36-a708-01b776e4dc1a/IGVFFI9918BQUQ.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-BinE-PCR1_S77_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6354LMIX/",
"accession": "IGVFFI6354LMIX",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF3-BinE-PCR3_S173"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T15:27:28.274476+00:00",
"file_format": "fastq",
"file_size": 16028375,
"href": "/sequence-files/IGVFFI6354LMIX/@@download/IGVFFI6354LMIX.fastq.gz",
"md5sum": "f40046b78fb288bc4d6789617b3230c2",
"s3_uri": "s3://igvf-files/2024/06/03/df228793-58c6-4b3d-8c71-de28236e3941/IGVFFI6354LMIX.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-BinE-PCR3_S173_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9827KBGQ/",
"accession": "IGVFFI9827KBGQ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF3-BinE-PCR4_S179"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T15:27:45.421976+00:00",
"file_format": "fastq",
"file_size": 16364490,
"href": "/sequence-files/IGVFFI9827KBGQ/@@download/IGVFFI9827KBGQ.fastq.gz",
"md5sum": "c1512533024f41499be3e1415b979365",
"s3_uri": "s3://igvf-files/2024/06/03/cfb4c2fb-3329-4879-bbda-97a7161d11c2/IGVFFI9827KBGQ.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-BinE-PCR4_S179_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4320HANL/",
"accession": "IGVFFI4320HANL",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF3-BinE-PCR2_S83"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T15:27:11.653639+00:00",
"file_format": "fastq",
"file_size": 7094947,
"href": "/sequence-files/IGVFFI4320HANL/@@download/IGVFFI4320HANL.fastq.gz",
"md5sum": "b73956033aa6ec46333c7f602799a91c",
"s3_uri": "s3://igvf-files/2024/06/03/3e967958-8dd6-442a-a272-0604d929f9b3/IGVFFI4320HANL.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-BinE-PCR2_S83_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": "2024-07-10T19:45:31.081180+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9250VIBU/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9250VIBU",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF3-BinE-PCR1_S77",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF3-BinE-PCR2_S83",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF3-BinE-PCR3_S173",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF3-BinE-PCR4_S179"
],
"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 E for 80-90% 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": "2024-06-03T15:26:56.063680+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": "4ed9ab0d-bfc1-4b96-a96e-9ae7b4e500a2"
}