{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6512WYQI/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6512WYQI",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep1-BinA_AmpliconSequencing"
],
"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 [IGVFDS6512WYQI](/measurement-sets/IGVFDS6512WYQI/) 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/IGVFDS6512WYQI/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS6512WYQI](/measurement-sets/IGVFDS6512WYQI/) has sequence file(s) [IGVFFI5745QBHR](/sequence-files/IGVFFI5745QBHR/), [IGVFFI1139IHLH](/sequence-files/IGVFFI1139IHLH/), [IGVFFI0136OTDT](/sequence-files/IGVFFI0136OTDT/), [IGVFFI4494KFXL](/sequence-files/IGVFFI4494KFXL/), [IGVFFI4003YITL](/sequence-files/IGVFFI4003YITL/), [IGVFFI1414YBRQ](/sequence-files/IGVFFI1414YBRQ/), [IGVFFI5384FSBF](/sequence-files/IGVFFI5384FSBF/), [IGVFFI4061LXVU](/sequence-files/IGVFFI4061LXVU/), [IGVFFI8537FZCH](/sequence-files/IGVFFI8537FZCH/), [IGVFFI4324LJYO](/sequence-files/IGVFFI4324LJYO/), [IGVFFI6562TAVO](/sequence-files/IGVFFI6562TAVO/), [IGVFFI1885BVYA](/sequence-files/IGVFFI1885BVYA/), [IGVFFI5057DXME](/sequence-files/IGVFFI5057DXME/), [IGVFFI4400QBKK](/sequence-files/IGVFFI4400QBKK/), [IGVFFI7437LODB](/sequence-files/IGVFFI7437LODB/), [IGVFFI0452WPEQ](/sequence-files/IGVFFI0452WPEQ/), [IGVFFI1083POLS](/sequence-files/IGVFFI1083POLS/), [IGVFFI6016TUZX](/sequence-files/IGVFFI6016TUZX/), [IGVFFI7380TRYF](/sequence-files/IGVFFI7380TRYF/), [IGVFFI7610NJIM](/sequence-files/IGVFFI7610NJIM/), [IGVFFI7741EXIF](/sequence-files/IGVFFI7741EXIF/), [IGVFFI0047LQKS](/sequence-files/IGVFFI0047LQKS/), [IGVFFI9023NBCB](/sequence-files/IGVFFI9023NBCB/), [IGVFFI6617UQOP](/sequence-files/IGVFFI6617UQOP/), [IGVFFI1679PXVC](/sequence-files/IGVFFI1679PXVC/), [IGVFFI6616JFLU](/sequence-files/IGVFFI6616JFLU/), [IGVFFI8720XJIY](/sequence-files/IGVFFI8720XJIY/), [IGVFFI3108PVBW](/sequence-files/IGVFFI3108PVBW/), [IGVFFI6152IAFD](/sequence-files/IGVFFI6152IAFD/), [IGVFFI2535FCBT](/sequence-files/IGVFFI2535FCBT/), [IGVFFI9537WYWH](/sequence-files/IGVFFI9537WYWH/), [IGVFFI4085ZQTM](/sequence-files/IGVFFI4085ZQTM/), [IGVFFI2896HDIF](/sequence-files/IGVFFI2896HDIF/), [IGVFFI7046VMDB](/sequence-files/IGVFFI7046VMDB/), [IGVFFI4447EADR](/sequence-files/IGVFFI4447EADR/), [IGVFFI0084ZRJQ](/sequence-files/IGVFFI0084ZRJQ/), [IGVFFI9903ESRJ](/sequence-files/IGVFFI9903ESRJ/), [IGVFFI3486RTZQ](/sequence-files/IGVFFI3486RTZQ/), [IGVFFI4082DRPU](/sequence-files/IGVFFI4082DRPU/), [IGVFFI1073TOXL](/sequence-files/IGVFFI1073TOXL/), [IGVFFI9247SEHS](/sequence-files/IGVFFI9247SEHS/), [IGVFFI2011NVBD](/sequence-files/IGVFFI2011NVBD/), [IGVFFI2276DZMF](/sequence-files/IGVFFI2276DZMF/), [IGVFFI1033UKUQ](/sequence-files/IGVFFI1033UKUQ/), [IGVFFI6784YQJM](/sequence-files/IGVFFI6784YQJM/), [IGVFFI2341ZKXI](/sequence-files/IGVFFI2341ZKXI/), [IGVFFI6332XFLX](/sequence-files/IGVFFI6332XFLX/), [IGVFFI7686VAXO](/sequence-files/IGVFFI7686VAXO/) 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/IGVFDS6512WYQI/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS6512WYQI](/measurement-sets/IGVFDS6512WYQI/) has sequence file(s): [IGVFFI5745QBHR](/sequence-files/IGVFFI5745QBHR/), [IGVFFI1139IHLH](/sequence-files/IGVFFI1139IHLH/), [IGVFFI0136OTDT](/sequence-files/IGVFFI0136OTDT/), [IGVFFI4494KFXL](/sequence-files/IGVFFI4494KFXL/), [IGVFFI4003YITL](/sequence-files/IGVFFI4003YITL/), [IGVFFI1414YBRQ](/sequence-files/IGVFFI1414YBRQ/), [IGVFFI5384FSBF](/sequence-files/IGVFFI5384FSBF/), [IGVFFI4061LXVU](/sequence-files/IGVFFI4061LXVU/), [IGVFFI8537FZCH](/sequence-files/IGVFFI8537FZCH/), [IGVFFI4324LJYO](/sequence-files/IGVFFI4324LJYO/), [IGVFFI6562TAVO](/sequence-files/IGVFFI6562TAVO/), [IGVFFI1885BVYA](/sequence-files/IGVFFI1885BVYA/), [IGVFFI5057DXME](/sequence-files/IGVFFI5057DXME/), [IGVFFI4400QBKK](/sequence-files/IGVFFI4400QBKK/), [IGVFFI7437LODB](/sequence-files/IGVFFI7437LODB/), [IGVFFI0452WPEQ](/sequence-files/IGVFFI0452WPEQ/), [IGVFFI1083POLS](/sequence-files/IGVFFI1083POLS/), [IGVFFI6016TUZX](/sequence-files/IGVFFI6016TUZX/), [IGVFFI7380TRYF](/sequence-files/IGVFFI7380TRYF/), [IGVFFI7610NJIM](/sequence-files/IGVFFI7610NJIM/), [IGVFFI7741EXIF](/sequence-files/IGVFFI7741EXIF/), [IGVFFI0047LQKS](/sequence-files/IGVFFI0047LQKS/), [IGVFFI9023NBCB](/sequence-files/IGVFFI9023NBCB/), [IGVFFI6617UQOP](/sequence-files/IGVFFI6617UQOP/), [IGVFFI1679PXVC](/sequence-files/IGVFFI1679PXVC/), [IGVFFI6616JFLU](/sequence-files/IGVFFI6616JFLU/), [IGVFFI8720XJIY](/sequence-files/IGVFFI8720XJIY/), [IGVFFI3108PVBW](/sequence-files/IGVFFI3108PVBW/), [IGVFFI6152IAFD](/sequence-files/IGVFFI6152IAFD/), [IGVFFI2535FCBT](/sequence-files/IGVFFI2535FCBT/), [IGVFFI9537WYWH](/sequence-files/IGVFFI9537WYWH/), [IGVFFI4085ZQTM](/sequence-files/IGVFFI4085ZQTM/), [IGVFFI2896HDIF](/sequence-files/IGVFFI2896HDIF/), [IGVFFI7046VMDB](/sequence-files/IGVFFI7046VMDB/), [IGVFFI4447EADR](/sequence-files/IGVFFI4447EADR/), [IGVFFI0084ZRJQ](/sequence-files/IGVFFI0084ZRJQ/), [IGVFFI9903ESRJ](/sequence-files/IGVFFI9903ESRJ/), [IGVFFI3486RTZQ](/sequence-files/IGVFFI3486RTZQ/), [IGVFFI4082DRPU](/sequence-files/IGVFFI4082DRPU/), [IGVFFI1073TOXL](/sequence-files/IGVFFI1073TOXL/), [IGVFFI9247SEHS](/sequence-files/IGVFFI9247SEHS/), [IGVFFI2011NVBD](/sequence-files/IGVFFI2011NVBD/), [IGVFFI2276DZMF](/sequence-files/IGVFFI2276DZMF/), [IGVFFI1033UKUQ](/sequence-files/IGVFFI1033UKUQ/), [IGVFFI6784YQJM](/sequence-files/IGVFFI6784YQJM/), [IGVFFI2341ZKXI](/sequence-files/IGVFFI2341ZKXI/), [IGVFFI6332XFLX](/sequence-files/IGVFFI6332XFLX/), [IGVFFI7686VAXO](/sequence-files/IGVFFI7686VAXO/) which do not have any `seqspecs`. Sequence files in a file set associated with bulk data are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS6512WYQI/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM5627EEDY](/in-vitro-systems/IGVFSM5627EEDY/) has in progress subobject construct library set [IGVFDS6982DESN](/construct-library-sets/IGVFDS6982DESN/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM5627EEDY/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM5627EEDY](/in-vitro-systems/IGVFSM5627EEDY/) 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/IGVFSM5627EEDY/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS6512WYQI](/measurement-sets/IGVFDS6512WYQI/) has no cell sorting `auxiliary_sets`. CRISPR-based measurement sets that utilize flow cytometry are expected to link to a cell sorting auxiliary set.",
"level": 40,
"level_name": "WARNING",
"name": "audit_missing_auxiliary_set",
"path": "/measurement-sets/IGVFDS6512WYQI/"
}
]
},
"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/IGVFDS6982DESN/",
"accession": "IGVFDS6982DESN",
"file_set_type": "guide library",
"status": "in progress",
"summary": "guide (sgRNA) library targeting sequence variants in a genomic locus"
}
],
"control_file_sets": [
{
"@id": "/measurement-sets/IGVFDS5864UGFT/",
"accession": "IGVFDS5864UGFT",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-THP1-PE2_Exp2_NegControl_AmpliconSequencing"
],
"status": "released"
}
],
"control_for": [],
"creation_timestamp": "2023-11-30T22:49:51.869008+00:00",
"data_use_limitation_summaries": [
"no certificate"
],
"donors": [
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"accession": "IGVFDO7359LVPI",
"aliases": [
"igvf:donor_of_THP1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI5745QBHR/",
"accession": "IGVFFI5745QBHR",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep1-BinA-PCRrep7_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:38:36.349743+00:00",
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"file_size": 1471080,
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1139IHLH/",
"accession": "IGVFFI1139IHLH",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep1-BinA-PCRrep4_I1"
],
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"term_name": "Illumina NextSeq 550"
},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0136OTDT/",
"accession": "IGVFFI0136OTDT",
"aliases": [
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},
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},
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],
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},
{
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"aliases": [
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},
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"upload_status": "validated"
},
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"@id": "/sequence-files/IGVFFI1414YBRQ/",
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},
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},
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},
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8537FZCH/",
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],
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4324LJYO/",
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"aliases": [
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],
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"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep1-BinA-PCRrep11_S203_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7686VAXO/",
"accession": "IGVFFI7686VAXO",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep1-BinA-PCRrep4_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:37:17.204695+00:00",
"file_format": "fastq",
"file_size": 6011909,
"href": "/sequence-files/IGVFFI7686VAXO/@@download/IGVFFI7686VAXO.fastq.gz",
"md5sum": "5e7fc64c45985d89453ac804bbc45be2",
"s3_uri": "s3://igvf-files/2023/12/05/c3dfad84-80f1-40e9-873e-1cf88964cc28/IGVFFI7686VAXO.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep1-BinA-PCRrep4_S196_R2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS3423PSID/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"notes": "The readout 2e41e624-f6c7-4f0c-a07e-bc36cefdca39 was removed from this measurement set. This measurement set previously used Variant FlowFISH as a preferred_assay_title, but this enum is now removed. So it has been defaulted to Variant-EFFECTS.",
"preferred_assay_title": "Variant-EFFECTS",
"protocols": [
"https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1"
],
"release_timestamp": "2023-12-20T23:06:27.859072+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5627EEDY/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5627EEDY",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep1-BinA"
],
"classifications": [
"cell line"
],
"institutional_certificates": [],
"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"modality": "prime editing",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:THP-1"
],
"status": "released",
"summary": "THP-1",
"term_name": "THP-1"
}
],
"status": "released",
"summary": "Homo sapiens (male) THP-1 cell line (sorting details: FACS bin for 0-25% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T21:33:18.025927+00:00",
"summary": "CRISPR prime editing Variant-EFFECTS sorted on the expression of PPIF integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"targeted_genes": [
{
"@id": "/genes/ENSG00000108179/",
"geneid": "ENSG00000108179",
"name": "peptidylprolyl isomerase F",
"status": "released",
"symbol": "PPIF",
"synonyms": [
"PPIase F",
"peptidylprolyl isomerase F",
"Cyp-D",
"peptidyl-prolyl cis-trans isomerase F, mitochondrial",
"PPIF",
"CyP-M",
"cyclophilin F",
"peptidyl-prolyl cis-trans isomerase, mitochondrial",
"cyclophilin 3",
"cyclophilin D",
"rotamase F",
"mitochondrial cyclophilin",
"CypD",
"CYP3"
]
}
],
"uuid": "62e302cd-96a0-48f0-8acb-d9d5ea4f5165"
}