{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9308CBBI/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9308CBBI",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinC-PCR1_S15",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinC-PCR2_S21",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinC-PCR3_S111",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinC-PCR4_S117"
],
"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": "In vitro system [IGVFSM7071BULA](/in-vitro-systems/IGVFSM7071BULA/) 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/IGVFSM7071BULA/"
},
{
"category": "missing publication",
"detail": "Auxiliary set [IGVFDS4522DABT](/auxiliary-sets/IGVFDS4522DABT/) 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/IGVFDS4522DABT/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS9308CBBI](/measurement-sets/IGVFDS9308CBBI/) 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/IGVFDS9308CBBI/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS9308CBBI](/measurement-sets/IGVFDS9308CBBI/) has sequence file(s) [IGVFFI7621INKU](/sequence-files/IGVFFI7621INKU/), [IGVFFI7661OGMF](/sequence-files/IGVFFI7661OGMF/), [IGVFFI5281RKUY](/sequence-files/IGVFFI5281RKUY/), [IGVFFI2546PANA](/sequence-files/IGVFFI2546PANA/) 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/IGVFDS9308CBBI/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM7071BULA](/in-vitro-systems/IGVFSM7071BULA/) 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/IGVFSM7071BULA/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS4522DABT/",
"accession": "IGVFDS4522DABT",
"aliases": [
"jesse-engreitz:auxiliary_sortparams_CRUDO_KITLG-Auxin0hrs-FF2"
],
"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": "2024-05-16T17:32:57.967339+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/IGVFFI5915HQEK/",
"accession": "IGVFFI5915HQEK",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF2-BinC-PCR3_S111"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:07:06.827765+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI5915HQEK/@@download/IGVFFI5915HQEK.yaml.gz",
"md5sum": "7c908fbe1b43135897d1f6e295bb8aec",
"s3_uri": "s3://igvf-files/2024/06/11/f1997c14-a1c0-405b-85da-815d481005fe/IGVFFI5915HQEK.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF2-BinC-PCR3_S111.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI0383OYTL/",
"accession": "IGVFFI0383OYTL",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF2-BinC-PCR2_S21"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:06:53.295311+00:00",
"file_format": "yaml",
"file_size": 900,
"href": "/configuration-files/IGVFFI0383OYTL/@@download/IGVFFI0383OYTL.yaml.gz",
"md5sum": "6437b71900264a33d287e1b4c3d9f46e",
"s3_uri": "s3://igvf-files/2024/06/11/14d04f53-789f-44ce-a07c-81fcc9c79cd4/IGVFFI0383OYTL.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF2-BinC-PCR2_S21.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI5011CJLO/",
"accession": "IGVFFI5011CJLO",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF2-BinC-PCR1_S15"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:06:39.581219+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI5011CJLO/@@download/IGVFFI5011CJLO.yaml.gz",
"md5sum": "223767b67ed9e686b58d9f15a4d8f848",
"s3_uri": "s3://igvf-files/2024/06/11/d56f94f5-4493-463c-ac12-7fc1618f92c2/IGVFFI5011CJLO.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF2-BinC-PCR1_S15.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI0460DWZH/",
"accession": "IGVFFI0460DWZH",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF2-BinC-PCR4_S117"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:07:19.967412+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI0460DWZH/@@download/IGVFFI0460DWZH.yaml.gz",
"md5sum": "ed1e75f10a63f2450780dce338797628",
"s3_uri": "s3://igvf-files/2024/06/11/566285eb-cbf9-4db0-9982-b045981fbf0c/IGVFFI0460DWZH.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF2-BinC-PCR4_S117.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI7621INKU/",
"accession": "IGVFFI7621INKU",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF2-BinC-PCR3_S111"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:16:55.027578+00:00",
"file_format": "fastq",
"file_size": 19998267,
"href": "/sequence-files/IGVFFI7621INKU/@@download/IGVFFI7621INKU.fastq.gz",
"md5sum": "ebd5b2dfa9286aa6a34a34f0d636b72b",
"s3_uri": "s3://igvf-files/2024/06/01/f7118058-6f0e-4230-8399-cf60bbb201b5/IGVFFI7621INKU.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-FF2-BinC-PCR3_S111_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7661OGMF/",
"accession": "IGVFFI7661OGMF",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF2-BinC-PCR4_S117"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:17:13.386802+00:00",
"file_format": "fastq",
"file_size": 22508303,
"href": "/sequence-files/IGVFFI7661OGMF/@@download/IGVFFI7661OGMF.fastq.gz",
"md5sum": "611e84c1d7b76436aeef6af1f28c691a",
"s3_uri": "s3://igvf-files/2024/06/01/386ea676-72f7-44e5-9167-891f95b10ee2/IGVFFI7661OGMF.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-FF2-BinC-PCR4_S117_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5281RKUY/",
"accession": "IGVFFI5281RKUY",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF2-BinC-PCR1_S15"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:14:35.717978+00:00",
"file_format": "fastq",
"file_size": 6946133,
"href": "/sequence-files/IGVFFI5281RKUY/@@download/IGVFFI5281RKUY.fastq.gz",
"md5sum": "3f8c5522db417bd83f422dc66ee00d9d",
"s3_uri": "s3://igvf-files/2024/06/01/fc535ec7-9112-4d77-bc2e-0338806cabea/IGVFFI5281RKUY.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-FF2-BinC-PCR1_S15_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2546PANA/",
"accession": "IGVFFI2546PANA",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF2-BinC-PCR2_S21"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:14:53.237438+00:00",
"file_format": "fastq",
"file_size": 11153667,
"href": "/sequence-files/IGVFFI2546PANA/@@download/IGVFFI2546PANA.fastq.gz",
"md5sum": "bac918b2392acaac1a31582fb79f127a",
"s3_uri": "s3://igvf-files/2024/06/01/929e418e-cc00-48f2-aba6-628eacc7fc16/IGVFFI2546PANA.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-FF2-BinC-PCR2_S21_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": "2024-07-10T19:42:38.255382+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7071BULA/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7071BULA",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinC-PCR1_S15",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinC-PCR2_S21",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinC-PCR3_S111",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinC-PCR4_S117"
],
"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 C for 35-45% 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": "2024-06-01T02:14:35.717978+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": "b79423b5-cc56-4962-b95a-01ff4410a025"
}