{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2510KWUP/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2510KWUP",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinD-PCR1_S16",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinD-PCR2_S22",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinD-PCR3_S112",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinD-PCR4_S118"
],
"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 [IGVFDS2510KWUP](/measurement-sets/IGVFDS2510KWUP/) 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/IGVFDS2510KWUP/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS2510KWUP](/measurement-sets/IGVFDS2510KWUP/) has sequence file(s) [IGVFFI9622WBXB](/sequence-files/IGVFFI9622WBXB/), [IGVFFI6102KUNE](/sequence-files/IGVFFI6102KUNE/), [IGVFFI4672XFAS](/sequence-files/IGVFFI4672XFAS/), [IGVFFI4599HIHJ](/sequence-files/IGVFFI4599HIHJ/) 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/IGVFDS2510KWUP/"
},
{
"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": "In vitro system [IGVFSM0606BETP](/in-vitro-systems/IGVFSM0606BETP/) 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/IGVFSM0606BETP/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM0606BETP](/in-vitro-systems/IGVFSM0606BETP/) 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/IGVFSM0606BETP/"
}
]
},
"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": "2024-05-16T17:32:59.142486+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/IGVFFI3581TVFQ/",
"accession": "IGVFFI3581TVFQ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF2-BinD-PCR3_S112"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:07:09.069560+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI3581TVFQ/@@download/IGVFFI3581TVFQ.yaml.gz",
"md5sum": "b6cf895dcc597bec8f14df59924c73e0",
"s3_uri": "s3://igvf-files/2024/06/11/da3861e5-0c8a-48a3-be53-1cd502c8a1a8/IGVFFI3581TVFQ.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF2-BinD-PCR3_S112.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI6667BWUV/",
"accession": "IGVFFI6667BWUV",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF2-BinD-PCR1_S16"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:06:41.952024+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI6667BWUV/@@download/IGVFFI6667BWUV.yaml.gz",
"md5sum": "101dc43eae2b48c146ece9398835f307",
"s3_uri": "s3://igvf-files/2024/06/11/0369317f-4166-42ff-a7ab-6498dd27c3dc/IGVFFI6667BWUV.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF2-BinD-PCR1_S16.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI9622WBXB/",
"accession": "IGVFFI9622WBXB",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF2-BinD-PCR1_S16"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:14:38.789140+00:00",
"file_format": "fastq",
"file_size": 11473942,
"href": "/sequence-files/IGVFFI9622WBXB/@@download/IGVFFI9622WBXB.fastq.gz",
"md5sum": "bf98be68c7bb9b6fb47ad36628335daf",
"s3_uri": "s3://igvf-files/2024/06/01/0aa229f6-61a0-4fb2-bdef-55b3cecf4bd1/IGVFFI9622WBXB.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-BinD-PCR1_S16_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6102KUNE/",
"accession": "IGVFFI6102KUNE",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF2-BinD-PCR3_S112"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:16:58.162203+00:00",
"file_format": "fastq",
"file_size": 30096956,
"href": "/sequence-files/IGVFFI6102KUNE/@@download/IGVFFI6102KUNE.fastq.gz",
"md5sum": "3f3fb18437049bdf90fa4c55f48fa207",
"s3_uri": "s3://igvf-files/2024/06/01/51a8bf56-957c-4844-8456-2649bbd00118/IGVFFI6102KUNE.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-BinD-PCR3_S112_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4835VKQX/",
"accession": "IGVFFI4835VKQX",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF2-BinD-PCR2_S22"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:06:55.571127+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI4835VKQX/@@download/IGVFFI4835VKQX.yaml.gz",
"md5sum": "d9a62718cd35e1bf444d15ad05e55401",
"s3_uri": "s3://igvf-files/2024/06/11/711fd576-8866-4564-aa54-b0bf57dfaccc/IGVFFI4835VKQX.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF2-BinD-PCR2_S22.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI3027QSYI/",
"accession": "IGVFFI3027QSYI",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF2-BinD-PCR4_S118"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:07:22.295172+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI3027QSYI/@@download/IGVFFI3027QSYI.yaml.gz",
"md5sum": "179f69122ba333cff0243b5d8fb121c7",
"s3_uri": "s3://igvf-files/2024/06/11/d9c5211e-2caf-4455-8a3f-f99e408934f3/IGVFFI3027QSYI.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF2-BinD-PCR4_S118.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI4672XFAS/",
"accession": "IGVFFI4672XFAS",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF2-BinD-PCR4_S118"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:17:16.259036+00:00",
"file_format": "fastq",
"file_size": 25003973,
"href": "/sequence-files/IGVFFI4672XFAS/@@download/IGVFFI4672XFAS.fastq.gz",
"md5sum": "52df4d801cc80bcd8912387f5c823b8d",
"s3_uri": "s3://igvf-files/2024/06/01/62417d39-433a-4daa-a0fd-72250b173d41/IGVFFI4672XFAS.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-BinD-PCR4_S118_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4599HIHJ/",
"accession": "IGVFFI4599HIHJ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF2-BinD-PCR2_S22"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:14:56.162966+00:00",
"file_format": "fastq",
"file_size": 12681809,
"href": "/sequence-files/IGVFFI4599HIHJ/@@download/IGVFFI4599HIHJ.fastq.gz",
"md5sum": "546cb74407b4b3fffc77f6c1ae42ef08",
"s3_uri": "s3://igvf-files/2024/06/01/515fd2d7-e962-4373-a262-0673b4ba1975/IGVFFI4599HIHJ.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-BinD-PCR2_S22_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": "2024-07-10T19:42:44.284200+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0606BETP/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0606BETP",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinD-PCR1_S16",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinD-PCR2_S22",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinD-PCR3_S112",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinD-PCR4_S118"
],
"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 D for 55-65% 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": "2024-06-01T02:14:38.789140+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": "23efe5d1-c2c7-4f7a-9ec2-73f5079d8c4a"
}