{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4071SWQV/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4071SWQV",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF3-BinB-PCR1_S26",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF3-BinB-PCR2_S32",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF3-BinB-PCR3_S122",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF3-BinB-PCR4_S128"
],
"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 [IGVFDS4071SWQV](/measurement-sets/IGVFDS4071SWQV/) 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/IGVFDS4071SWQV/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS4071SWQV](/measurement-sets/IGVFDS4071SWQV/) has sequence file(s) [IGVFFI7218BQAT](/sequence-files/IGVFFI7218BQAT/), [IGVFFI6990ETYU](/sequence-files/IGVFFI6990ETYU/), [IGVFFI4574NUVT](/sequence-files/IGVFFI4574NUVT/), [IGVFFI4833WLGU](/sequence-files/IGVFFI4833WLGU/) 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/IGVFDS4071SWQV/"
},
{
"category": "missing publication",
"detail": "Auxiliary set [IGVFDS0329USVJ](/auxiliary-sets/IGVFDS0329USVJ/) 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/IGVFDS0329USVJ/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM1489ABUX](/in-vitro-systems/IGVFSM1489ABUX/) 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/IGVFSM1489ABUX/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM1489ABUX](/in-vitro-systems/IGVFSM1489ABUX/) 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/IGVFSM1489ABUX/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS0329USVJ/",
"accession": "IGVFDS0329USVJ",
"aliases": [
"jesse-engreitz:auxiliary_sortparams_CRUDO_KITLG-Auxin0hrs-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": "2024-05-16T17:33:20.389510+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/IGVFFI2578ZJHZ/",
"accession": "IGVFFI2578ZJHZ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF3-BinB-PCR1_S26"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:07:31.138230+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI2578ZJHZ/@@download/IGVFFI2578ZJHZ.yaml.gz",
"md5sum": "050e385154ab2d301b2cb7980c87368f",
"s3_uri": "s3://igvf-files/2024/06/11/b61ae897-3d26-4fc0-ae1b-4f17800821ea/IGVFFI2578ZJHZ.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF3-BinB-PCR1_S26.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI2162SQTL/",
"accession": "IGVFFI2162SQTL",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF3-BinB-PCR4_S128"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:08:11.130668+00:00",
"file_format": "yaml",
"file_size": 904,
"href": "/configuration-files/IGVFFI2162SQTL/@@download/IGVFFI2162SQTL.yaml.gz",
"md5sum": "49b0435ae249033478813d4e22625ea8",
"s3_uri": "s3://igvf-files/2024/06/11/a09b285f-930b-44e5-b78d-5544ee93786c/IGVFFI2162SQTL.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF3-BinB-PCR4_S128.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI0234RCMR/",
"accession": "IGVFFI0234RCMR",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF3-BinB-PCR3_S122"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:07:57.966974+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI0234RCMR/@@download/IGVFFI0234RCMR.yaml.gz",
"md5sum": "f9a886b7bd878aadc623885408e23019",
"s3_uri": "s3://igvf-files/2024/06/11/fab9e5f5-0ff7-4d19-9f36-8122d6cdeed1/IGVFFI0234RCMR.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF3-BinB-PCR3_S122.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI2867ZNBX/",
"accession": "IGVFFI2867ZNBX",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF3-BinB-PCR2_S32"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:07:44.769332+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI2867ZNBX/@@download/IGVFFI2867ZNBX.yaml.gz",
"md5sum": "d0606a443a4cb26fdc7c82c4da1bb786",
"s3_uri": "s3://igvf-files/2024/06/11/9bde290b-7bfb-4b3d-b707-5c7c1cf658e7/IGVFFI2867ZNBX.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF3-BinB-PCR2_S32.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI7218BQAT/",
"accession": "IGVFFI7218BQAT",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF3-BinB-PCR2_S32"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:17:45.653500+00:00",
"file_format": "fastq",
"file_size": 9925743,
"href": "/sequence-files/IGVFFI7218BQAT/@@download/IGVFFI7218BQAT.fastq.gz",
"md5sum": "e8f5a9fc6af7e5cd49c5f054bee5f18d",
"s3_uri": "s3://igvf-files/2024/06/01/2ae4b740-4f4a-4a23-9867-b70cc9e2aca2/IGVFFI7218BQAT.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-FF3-BinB-PCR2_S32_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6990ETYU/",
"accession": "IGVFFI6990ETYU",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF3-BinB-PCR4_S128"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:18:21.708058+00:00",
"file_format": "fastq",
"file_size": 18048316,
"href": "/sequence-files/IGVFFI6990ETYU/@@download/IGVFFI6990ETYU.fastq.gz",
"md5sum": "2722f6154d6b3c26089d238a183e6386",
"s3_uri": "s3://igvf-files/2024/06/01/9922e04b-733d-40d1-9b42-e5d27488976c/IGVFFI6990ETYU.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-FF3-BinB-PCR4_S128_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4574NUVT/",
"accession": "IGVFFI4574NUVT",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF3-BinB-PCR1_S26"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:17:28.299212+00:00",
"file_format": "fastq",
"file_size": 9128704,
"href": "/sequence-files/IGVFFI4574NUVT/@@download/IGVFFI4574NUVT.fastq.gz",
"md5sum": "2ded152e589592023d5763297038ed95",
"s3_uri": "s3://igvf-files/2024/06/01/a01cec2d-34f6-4f66-91ac-0dbe2b207324/IGVFFI4574NUVT.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina HiSeq 2500"
},
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF3-BinB-PCR1_S26_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4833WLGU/",
"accession": "IGVFFI4833WLGU",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF3-BinB-PCR3_S122"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:18:03.577696+00:00",
"file_format": "fastq",
"file_size": 22102045,
"href": "/sequence-files/IGVFFI4833WLGU/@@download/IGVFFI4833WLGU.fastq.gz",
"md5sum": "bbcb45ea80cede994732c95b3386a6e4",
"s3_uri": "s3://igvf-files/2024/06/01/55fa7667-3cd9-4694-a6b9-bd7564f14d0e/IGVFFI4833WLGU.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-FF3-BinB-PCR3_S122_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": "2024-07-10T19:43:07.332732+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1489ABUX/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1489ABUX",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF3-BinB-PCR1_S26",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF3-BinB-PCR2_S32",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF3-BinB-PCR3_S122",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF3-BinB-PCR4_S128"
],
"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 B for 10-20% 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": "2024-06-01T02:17:28.299212+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": "7cd79b3e-1fb9-458d-8ce5-1561e3d8d78d"
}