{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4649YECB/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4649YECB",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinA-PCR1_S13",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinA-PCR2_S19",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinA-PCR4_S115",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinB-PCR3_S109"
],
"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 [IGVFDS4649YECB](/measurement-sets/IGVFDS4649YECB/) 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/IGVFDS4649YECB/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS4649YECB](/measurement-sets/IGVFDS4649YECB/) has sequence file(s) [IGVFFI8656RWXA](/sequence-files/IGVFFI8656RWXA/), [IGVFFI6736AYSD](/sequence-files/IGVFFI6736AYSD/), [IGVFFI5346NUQZ](/sequence-files/IGVFFI5346NUQZ/), [IGVFFI3592XQZL](/sequence-files/IGVFFI3592XQZL/) 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/IGVFDS4649YECB/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM8346JZPG](/in-vitro-systems/IGVFSM8346JZPG/) 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/IGVFSM8346JZPG/"
},
{
"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/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM8346JZPG](/in-vitro-systems/IGVFSM8346JZPG/) 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/IGVFSM8346JZPG/"
}
]
},
"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": "2024-05-16T17:32:55.948515+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/IGVFFI3114INON/",
"accession": "IGVFFI3114INON",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF2-BinA-PCR4_S115"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:07:15.539236+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI3114INON/@@download/IGVFFI3114INON.yaml.gz",
"md5sum": "c8b2152ce0981d5f306be8f3dcf43c1c",
"s3_uri": "s3://igvf-files/2024/06/11/16ba4143-51dd-49f3-86d4-a9c9318a8d7f/IGVFFI3114INON.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF2-BinA-PCR4_S115.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI6590TUUT/",
"accession": "IGVFFI6590TUUT",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF2-BinA-PCR2_S19"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:06:48.568457+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI6590TUUT/@@download/IGVFFI6590TUUT.yaml.gz",
"md5sum": "4b937b2133224e7fafa67267d31e4e47",
"s3_uri": "s3://igvf-files/2024/06/11/99a1c76a-8aee-4ed5-b4ae-34d7b3b37b6e/IGVFFI6590TUUT.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF2-BinA-PCR2_S19.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI0792VIBF/",
"accession": "IGVFFI0792VIBF",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF2-BinA-PCR3_S109"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:07:02.254578+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI0792VIBF/@@download/IGVFFI0792VIBF.yaml.gz",
"md5sum": "250d1403d072e5707185c1d9441bdec1",
"s3_uri": "s3://igvf-files/2024/06/11/fa25a008-32d0-4577-9660-dbcf079cc3b9/IGVFFI0792VIBF.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF2-BinA-PCR3_S109.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI6317BSBL/",
"accession": "IGVFFI6317BSBL",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF2-BinA-PCR1_S13"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:06:35.312395+00:00",
"file_format": "yaml",
"file_size": 904,
"href": "/configuration-files/IGVFFI6317BSBL/@@download/IGVFFI6317BSBL.yaml.gz",
"md5sum": "1db31c4cca7ab75d704fc093b96c9e58",
"s3_uri": "s3://igvf-files/2024/06/11/09d17721-93d8-4229-987a-df3490d496dd/IGVFFI6317BSBL.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF2-BinA-PCR1_S13.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI8656RWXA/",
"accession": "IGVFFI8656RWXA",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF2-BinA-PCR3_S109"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:16:48.948175+00:00",
"file_format": "fastq",
"file_size": 39042526,
"href": "/sequence-files/IGVFFI8656RWXA/@@download/IGVFFI8656RWXA.fastq.gz",
"md5sum": "1114e18c10131293e1cc585e2b615285",
"s3_uri": "s3://igvf-files/2024/06/01/4a6b87d9-f754-4ec6-9dd7-6e3b3027b4de/IGVFFI8656RWXA.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-BinA-PCR3_S109_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6736AYSD/",
"accession": "IGVFFI6736AYSD",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF2-BinA-PCR2_S19"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:14:47.344896+00:00",
"file_format": "fastq",
"file_size": 10477762,
"href": "/sequence-files/IGVFFI6736AYSD/@@download/IGVFFI6736AYSD.fastq.gz",
"md5sum": "a51d70d9c8e7ea71bd725c6ff744dd87",
"s3_uri": "s3://igvf-files/2024/06/01/6f55cbd7-8038-4b9e-9eca-85240a2c7fe5/IGVFFI6736AYSD.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-BinA-PCR2_S19_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5346NUQZ/",
"accession": "IGVFFI5346NUQZ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF2-BinA-PCR4_S115"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:17:07.282030+00:00",
"file_format": "fastq",
"file_size": 22023359,
"href": "/sequence-files/IGVFFI5346NUQZ/@@download/IGVFFI5346NUQZ.fastq.gz",
"md5sum": "466392084c3886796fcc2604074f8087",
"s3_uri": "s3://igvf-files/2024/06/01/af6314c3-7a6d-4b1d-88ab-5285ac97d6c8/IGVFFI5346NUQZ.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-BinA-PCR4_S115_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3592XQZL/",
"accession": "IGVFFI3592XQZL",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF2-BinA-PCR1_S13"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:14:29.539667+00:00",
"file_format": "fastq",
"file_size": 13456146,
"href": "/sequence-files/IGVFFI3592XQZL/@@download/IGVFFI3592XQZL.fastq.gz",
"md5sum": "90ffdd81691bea12a68129807f9504d6",
"s3_uri": "s3://igvf-files/2024/06/01/422b3fa6-d82b-46b3-86bf-705a9ccca1a4/IGVFFI3592XQZL.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-BinA-PCR1_S13_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": "2024-07-10T19:42:27.196820+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8346JZPG/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8346JZPG",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinA-PCR1_S13",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinA-PCR2_S19",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinA-PCR4_S115",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinA-PCR3_S109"
],
"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 A for 0-10% 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": "2024-06-01T02:14:29.539667+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": "906459f8-2842-4af3-ac3e-bef80757967a"
}