{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0600IKJB/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0600IKJB",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF3-BinF-PCR1_S30",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF3-BinF-PCR2_S36",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF3-BinF-PCR3_S126",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF3-BinF-PCR4_S132"
],
"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 [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": "Measurement set [IGVFDS0600IKJB](/measurement-sets/IGVFDS0600IKJB/) 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/IGVFDS0600IKJB/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS0600IKJB](/measurement-sets/IGVFDS0600IKJB/) has sequence file(s) [IGVFFI8461PESG](/sequence-files/IGVFFI8461PESG/), [IGVFFI1402KSIW](/sequence-files/IGVFFI1402KSIW/), [IGVFFI1359HHUE](/sequence-files/IGVFFI1359HHUE/), [IGVFFI1150JCHT](/sequence-files/IGVFFI1150JCHT/) 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/IGVFDS0600IKJB/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM7141IWGF](/in-vitro-systems/IGVFSM7141IWGF/) 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/IGVFSM7141IWGF/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM7141IWGF](/in-vitro-systems/IGVFSM7141IWGF/) 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/IGVFSM7141IWGF/"
}
]
},
"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": "2024-05-16T17:33:24.228164+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/IGVFFI4265GEQC/",
"accession": "IGVFFI4265GEQC",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF3-BinF-PCR1_S30"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:07:40.336209+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI4265GEQC/@@download/IGVFFI4265GEQC.yaml.gz",
"md5sum": "5232b1f7daff7299da538d96f3f4a487",
"s3_uri": "s3://igvf-files/2024/06/11/f5aee5c0-a565-4b78-bc74-5dcc4cddd3d7/IGVFFI4265GEQC.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF3-BinF-PCR1_S30.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI4893JIOO/",
"accession": "IGVFFI4893JIOO",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF3-BinF-PCR3_S126"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:08:06.662117+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI4893JIOO/@@download/IGVFFI4893JIOO.yaml.gz",
"md5sum": "1bebcf68a396c99a998232772f8c571c",
"s3_uri": "s3://igvf-files/2024/06/11/1491fc12-14a1-421d-9eba-4cc71534fcb7/IGVFFI4893JIOO.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF3-BinF-PCR3_S126.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI8549VEWO/",
"accession": "IGVFFI8549VEWO",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF3-BinF-PCR4_S132"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:08:19.954150+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI8549VEWO/@@download/IGVFFI8549VEWO.yaml.gz",
"md5sum": "88bedefd37d68135f22ef8a8a7338e61",
"s3_uri": "s3://igvf-files/2024/06/11/6d8d5d64-a4d0-47a7-b97c-691ab6b85dab/IGVFFI8549VEWO.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF3-BinF-PCR4_S132.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI5393CUFG/",
"accession": "IGVFFI5393CUFG",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF3-BinF-PCR2_S36"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:07:53.508073+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI5393CUFG/@@download/IGVFFI5393CUFG.yaml.gz",
"md5sum": "199d95f000eae9fe4065bb9ccf6d75d5",
"s3_uri": "s3://igvf-files/2024/06/11/f452fa10-19ed-41c8-8be4-56004e3d1c91/IGVFFI5393CUFG.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF3-BinF-PCR2_S36.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI8461PESG/",
"accession": "IGVFFI8461PESG",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF3-BinF-PCR2_S36"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:17:57.746625+00:00",
"file_format": "fastq",
"file_size": 8943891,
"href": "/sequence-files/IGVFFI8461PESG/@@download/IGVFFI8461PESG.fastq.gz",
"md5sum": "7dd7d6906ebccceccc79ab47b58deaf9",
"s3_uri": "s3://igvf-files/2024/06/01/98635695-ddcf-4a47-8660-bd6e220b521b/IGVFFI8461PESG.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-BinF-PCR2_S36_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1402KSIW/",
"accession": "IGVFFI1402KSIW",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF3-BinF-PCR4_S132"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:18:37.897313+00:00",
"file_format": "fastq",
"file_size": 20561098,
"href": "/sequence-files/IGVFFI1402KSIW/@@download/IGVFFI1402KSIW.fastq.gz",
"md5sum": "945c745e6f584e5e1c349b97e4faa87a",
"s3_uri": "s3://igvf-files/2024/06/01/84596e94-1e29-4049-9787-cfd61e28f5ec/IGVFFI1402KSIW.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-BinF-PCR4_S132_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1359HHUE/",
"accession": "IGVFFI1359HHUE",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF3-BinF-PCR3_S126"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:18:15.672424+00:00",
"file_format": "fastq",
"file_size": 27179584,
"href": "/sequence-files/IGVFFI1359HHUE/@@download/IGVFFI1359HHUE.fastq.gz",
"md5sum": "85215ff706ad0382c1d52d49a854b596",
"s3_uri": "s3://igvf-files/2024/06/01/dff0393e-fa3d-4588-ab17-ad64dfd42d10/IGVFFI1359HHUE.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-BinF-PCR3_S126_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1150JCHT/",
"accession": "IGVFFI1150JCHT",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF3-BinF-PCR1_S30"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:17:39.461501+00:00",
"file_format": "fastq",
"file_size": 12726879,
"href": "/sequence-files/IGVFFI1150JCHT/@@download/IGVFFI1150JCHT.fastq.gz",
"md5sum": "73d6ddab75cdeb9cc28a40b3cbe4337c",
"s3_uri": "s3://igvf-files/2024/06/01/a3bf18b1-ae51-49ef-b4eb-4b6333194aa8/IGVFFI1150JCHT.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-BinF-PCR1_S30_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": "2024-07-10T19:43:27.648062+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7141IWGF/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7141IWGF",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF3-BinF-PCR1_S30",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF3-BinF-PCR2_S36",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF3-BinF-PCR3_S126",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF3-BinF-PCR4_S132"
],
"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 F for 80-100% 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": "2024-06-01T02:17:39.461501+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": "4c9a4850-c8b4-4031-8a32-e117de0b0a35"
}