{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2273HBVA/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2273HBVA",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF4-BinB-PCR1_S86",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF4-BinB-PCR2_S92",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF4-BinB-PCR3_S182",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF4-BinB-PCR4_S188"
],
"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 [IGVFDS2273HBVA](/measurement-sets/IGVFDS2273HBVA/) 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/IGVFDS2273HBVA/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS2273HBVA](/measurement-sets/IGVFDS2273HBVA/) has sequence file(s) [IGVFFI8664EIWJ](/sequence-files/IGVFFI8664EIWJ/), [IGVFFI3502JPZE](/sequence-files/IGVFFI3502JPZE/), [IGVFFI9283IUBN](/sequence-files/IGVFFI9283IUBN/), [IGVFFI7849AHAB](/sequence-files/IGVFFI7849AHAB/) 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/IGVFDS2273HBVA/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM5182LFZS](/in-vitro-systems/IGVFSM5182LFZS/) 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/IGVFSM5182LFZS/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM5182LFZS](/in-vitro-systems/IGVFSM5182LFZS/) 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/IGVFSM5182LFZS/"
}
]
},
"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": "2024-05-16T17:57:42.152531+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/IGVFFI7128OXNM/",
"accession": "IGVFFI7128OXNM",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF4-BinB-PCR3_S182"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:12:48.789391+00:00",
"file_format": "yaml",
"file_size": 904,
"href": "/configuration-files/IGVFFI7128OXNM/@@download/IGVFFI7128OXNM.yaml.gz",
"md5sum": "0e477cb2ba4e08d16ea1178856ad3f61",
"s3_uri": "s3://igvf-files/2024/06/11/52d26be3-fcad-42eb-9575-45cbef66bcd0/IGVFFI7128OXNM.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF4-BinB-PCR3_S182.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI5599GUUW/",
"accession": "IGVFFI5599GUUW",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF4-BinB-PCR2_S92"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:12:34.058352+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI5599GUUW/@@download/IGVFFI5599GUUW.yaml.gz",
"md5sum": "7849bcf09ea957be39299c35a72a4b4f",
"s3_uri": "s3://igvf-files/2024/06/11/b2bd19c0-dbb4-4485-bc18-5d432670ccee/IGVFFI5599GUUW.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF4-BinB-PCR2_S92.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI2941VKHY/",
"accession": "IGVFFI2941VKHY",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF4-BinB-PCR4_S188"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:13:03.582219+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI2941VKHY/@@download/IGVFFI2941VKHY.yaml.gz",
"md5sum": "4d379a33edc33da1cf8b52ce15c310c2",
"s3_uri": "s3://igvf-files/2024/06/11/79e1e338-b2ec-4bcf-ab52-6f4573d28d48/IGVFFI2941VKHY.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF4-BinB-PCR4_S188.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI2146QZKY/",
"accession": "IGVFFI2146QZKY",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF4-BinB-PCR1_S86"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:12:19.546139+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI2146QZKY/@@download/IGVFFI2146QZKY.yaml.gz",
"md5sum": "dc74707697559d846c9bd6fd19cb20b2",
"s3_uri": "s3://igvf-files/2024/06/11/60e4346c-b63d-440b-94a1-e7b6d08a8296/IGVFFI2146QZKY.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF4-BinB-PCR1_S86.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI8664EIWJ/",
"accession": "IGVFFI8664EIWJ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF4-BinB-PCR1_S86"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T15:27:53.904045+00:00",
"file_format": "fastq",
"file_size": 7015668,
"href": "/sequence-files/IGVFFI8664EIWJ/@@download/IGVFFI8664EIWJ.fastq.gz",
"md5sum": "c49a7d0d6dbb6516a26689dc4dd6f06b",
"s3_uri": "s3://igvf-files/2024/06/03/e5ee4791-c736-470a-a434-fe33e2e5e494/IGVFFI8664EIWJ.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-BinB-PCR1_S86_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3502JPZE/",
"accession": "IGVFFI3502JPZE",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF4-BinB-PCR3_S182"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T15:28:25.961215+00:00",
"file_format": "fastq",
"file_size": 11929855,
"href": "/sequence-files/IGVFFI3502JPZE/@@download/IGVFFI3502JPZE.fastq.gz",
"md5sum": "cc6fdbd286df38b033dc0650ec8ced8d",
"s3_uri": "s3://igvf-files/2024/06/03/0070e984-e509-4452-9fb9-709bad8eee4a/IGVFFI3502JPZE.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-BinB-PCR3_S182_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9283IUBN/",
"accession": "IGVFFI9283IUBN",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF4-BinB-PCR4_S188"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T15:28:42.415136+00:00",
"file_format": "fastq",
"file_size": 9036588,
"href": "/sequence-files/IGVFFI9283IUBN/@@download/IGVFFI9283IUBN.fastq.gz",
"md5sum": "f112a07ee844d2108d768c2029ac63b5",
"s3_uri": "s3://igvf-files/2024/06/03/aa553202-7028-4d64-887a-a9e6f35ab1ce/IGVFFI9283IUBN.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-BinB-PCR4_S188_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7849AHAB/",
"accession": "IGVFFI7849AHAB",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF4-BinB-PCR2_S92"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T15:28:09.762574+00:00",
"file_format": "fastq",
"file_size": 4290605,
"href": "/sequence-files/IGVFFI7849AHAB/@@download/IGVFFI7849AHAB.fastq.gz",
"md5sum": "417d7f681b5b982d0771a55b2ce8378f",
"s3_uri": "s3://igvf-files/2024/06/03/006c0460-dd89-4347-a972-86f7478bf9ac/IGVFFI7849AHAB.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-BinB-PCR2_S92_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": "2024-07-10T19:45:48.148878+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5182LFZS/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5182LFZS",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF4-BinB-PCR1_S86",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF4-BinB-PCR2_S92",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF4-BinB-PCR3_S182",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF4-BinB-PCR4_S188"
],
"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 B for 10-20% 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": "2024-06-03T15:27:53.904045+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": "4522c117-e717-420e-81da-17437fc7e99b"
}