{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1319XVLL/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1319XVLL",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep2-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 sequencing kit",
"detail": "Measurement set [IGVFDS1319XVLL](/measurement-sets/IGVFDS1319XVLL/) has sequence file(s) [IGVFFI6157RLIA](/sequence-files/IGVFFI6157RLIA/), [IGVFFI0416YRLS](/sequence-files/IGVFFI0416YRLS/), [IGVFFI1886CXGZ](/sequence-files/IGVFFI1886CXGZ/), [IGVFFI9419YLFW](/sequence-files/IGVFFI9419YLFW/), [IGVFFI1999EXLH](/sequence-files/IGVFFI1999EXLH/), [IGVFFI0425TAES](/sequence-files/IGVFFI0425TAES/), [IGVFFI7039BUWJ](/sequence-files/IGVFFI7039BUWJ/), [IGVFFI0950CPRT](/sequence-files/IGVFFI0950CPRT/), [IGVFFI2628GCOT](/sequence-files/IGVFFI2628GCOT/), [IGVFFI1546NHZH](/sequence-files/IGVFFI1546NHZH/), [IGVFFI7710LIFV](/sequence-files/IGVFFI7710LIFV/), [IGVFFI9674BACC](/sequence-files/IGVFFI9674BACC/), [IGVFFI6508GSWD](/sequence-files/IGVFFI6508GSWD/), [IGVFFI6180DGKA](/sequence-files/IGVFFI6180DGKA/), [IGVFFI9206AUFI](/sequence-files/IGVFFI9206AUFI/), [IGVFFI4044PBRP](/sequence-files/IGVFFI4044PBRP/), [IGVFFI7554YPPS](/sequence-files/IGVFFI7554YPPS/), [IGVFFI8777MXXY](/sequence-files/IGVFFI8777MXXY/), [IGVFFI9241FNZY](/sequence-files/IGVFFI9241FNZY/), [IGVFFI3503BPKN](/sequence-files/IGVFFI3503BPKN/), [IGVFFI0019XPES](/sequence-files/IGVFFI0019XPES/), [IGVFFI0576ECSI](/sequence-files/IGVFFI0576ECSI/), [IGVFFI8033WMRT](/sequence-files/IGVFFI8033WMRT/), [IGVFFI5873SDKS](/sequence-files/IGVFFI5873SDKS/), [IGVFFI9724EAAQ](/sequence-files/IGVFFI9724EAAQ/), [IGVFFI9492AZKJ](/sequence-files/IGVFFI9492AZKJ/), [IGVFFI2564NSJV](/sequence-files/IGVFFI2564NSJV/), [IGVFFI8009HURM](/sequence-files/IGVFFI8009HURM/), [IGVFFI6909ADER](/sequence-files/IGVFFI6909ADER/), [IGVFFI4092GCVZ](/sequence-files/IGVFFI4092GCVZ/), [IGVFFI5700GLSH](/sequence-files/IGVFFI5700GLSH/), [IGVFFI9956YVYV](/sequence-files/IGVFFI9956YVYV/), [IGVFFI3712MJHT](/sequence-files/IGVFFI3712MJHT/), [IGVFFI6519RCQL](/sequence-files/IGVFFI6519RCQL/), [IGVFFI2843CVQX](/sequence-files/IGVFFI2843CVQX/), [IGVFFI5396LVCV](/sequence-files/IGVFFI5396LVCV/), [IGVFFI3451KSGC](/sequence-files/IGVFFI3451KSGC/), [IGVFFI2873DIIR](/sequence-files/IGVFFI2873DIIR/), [IGVFFI9949DCGR](/sequence-files/IGVFFI9949DCGR/), [IGVFFI0464IKFP](/sequence-files/IGVFFI0464IKFP/), [IGVFFI3201AANW](/sequence-files/IGVFFI3201AANW/), [IGVFFI3189ONQJ](/sequence-files/IGVFFI3189ONQJ/), [IGVFFI7767YDDR](/sequence-files/IGVFFI7767YDDR/), [IGVFFI3962IEJM](/sequence-files/IGVFFI3962IEJM/), [IGVFFI6761LLIA](/sequence-files/IGVFFI6761LLIA/), [IGVFFI3435YJPI](/sequence-files/IGVFFI3435YJPI/), [IGVFFI9435OMZV](/sequence-files/IGVFFI9435OMZV/), [IGVFFI6700IZYS](/sequence-files/IGVFFI6700IZYS/) 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/IGVFDS1319XVLL/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS1319XVLL](/measurement-sets/IGVFDS1319XVLL/) has sequence file(s): [IGVFFI6157RLIA](/sequence-files/IGVFFI6157RLIA/), [IGVFFI0416YRLS](/sequence-files/IGVFFI0416YRLS/), [IGVFFI1886CXGZ](/sequence-files/IGVFFI1886CXGZ/), [IGVFFI9419YLFW](/sequence-files/IGVFFI9419YLFW/), [IGVFFI1999EXLH](/sequence-files/IGVFFI1999EXLH/), [IGVFFI0425TAES](/sequence-files/IGVFFI0425TAES/), [IGVFFI7039BUWJ](/sequence-files/IGVFFI7039BUWJ/), [IGVFFI0950CPRT](/sequence-files/IGVFFI0950CPRT/), [IGVFFI2628GCOT](/sequence-files/IGVFFI2628GCOT/), [IGVFFI1546NHZH](/sequence-files/IGVFFI1546NHZH/), [IGVFFI7710LIFV](/sequence-files/IGVFFI7710LIFV/), [IGVFFI9674BACC](/sequence-files/IGVFFI9674BACC/), [IGVFFI6508GSWD](/sequence-files/IGVFFI6508GSWD/), [IGVFFI6180DGKA](/sequence-files/IGVFFI6180DGKA/), [IGVFFI9206AUFI](/sequence-files/IGVFFI9206AUFI/), [IGVFFI4044PBRP](/sequence-files/IGVFFI4044PBRP/), [IGVFFI7554YPPS](/sequence-files/IGVFFI7554YPPS/), [IGVFFI8777MXXY](/sequence-files/IGVFFI8777MXXY/), [IGVFFI9241FNZY](/sequence-files/IGVFFI9241FNZY/), [IGVFFI3503BPKN](/sequence-files/IGVFFI3503BPKN/), [IGVFFI0019XPES](/sequence-files/IGVFFI0019XPES/), [IGVFFI0576ECSI](/sequence-files/IGVFFI0576ECSI/), [IGVFFI8033WMRT](/sequence-files/IGVFFI8033WMRT/), [IGVFFI5873SDKS](/sequence-files/IGVFFI5873SDKS/), [IGVFFI9724EAAQ](/sequence-files/IGVFFI9724EAAQ/), [IGVFFI9492AZKJ](/sequence-files/IGVFFI9492AZKJ/), [IGVFFI2564NSJV](/sequence-files/IGVFFI2564NSJV/), [IGVFFI8009HURM](/sequence-files/IGVFFI8009HURM/), [IGVFFI6909ADER](/sequence-files/IGVFFI6909ADER/), [IGVFFI4092GCVZ](/sequence-files/IGVFFI4092GCVZ/), [IGVFFI5700GLSH](/sequence-files/IGVFFI5700GLSH/), [IGVFFI9956YVYV](/sequence-files/IGVFFI9956YVYV/), [IGVFFI3712MJHT](/sequence-files/IGVFFI3712MJHT/), [IGVFFI6519RCQL](/sequence-files/IGVFFI6519RCQL/), [IGVFFI2843CVQX](/sequence-files/IGVFFI2843CVQX/), [IGVFFI5396LVCV](/sequence-files/IGVFFI5396LVCV/), [IGVFFI3451KSGC](/sequence-files/IGVFFI3451KSGC/), [IGVFFI2873DIIR](/sequence-files/IGVFFI2873DIIR/), [IGVFFI9949DCGR](/sequence-files/IGVFFI9949DCGR/), [IGVFFI0464IKFP](/sequence-files/IGVFFI0464IKFP/), [IGVFFI3201AANW](/sequence-files/IGVFFI3201AANW/), [IGVFFI3189ONQJ](/sequence-files/IGVFFI3189ONQJ/), [IGVFFI7767YDDR](/sequence-files/IGVFFI7767YDDR/), [IGVFFI3962IEJM](/sequence-files/IGVFFI3962IEJM/), [IGVFFI6761LLIA](/sequence-files/IGVFFI6761LLIA/), [IGVFFI3435YJPI](/sequence-files/IGVFFI3435YJPI/), [IGVFFI9435OMZV](/sequence-files/IGVFFI9435OMZV/), [IGVFFI6700IZYS](/sequence-files/IGVFFI6700IZYS/) 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/IGVFDS1319XVLL/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS1319XVLL](/measurement-sets/IGVFDS1319XVLL/) 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/IGVFDS1319XVLL/"
}
]
},
"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/IGVFDS4955GEYO/",
"accession": "IGVFDS4955GEYO",
"file_set_type": "guide library",
"status": "preview",
"summary": "guide (sgRNA) library targeting sequence variants in a genomic locus"
}
],
"control_file_sets": [
{
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"accession": "IGVFDS4103BJLT",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-THP1-PE2_Exp4_NegControl_AmpliconSequencing"
],
"status": "preview"
}
],
"control_for": [],
"creation_timestamp": "2024-11-25T23:52:26.064614+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",
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},
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240426S024-Enhancer-THP1-PPIF_Enhancer_val_guides-Amp_PPIF_enhancer-BioRep1-FFrep2-BinA-PCRrep7_S469_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9435OMZV/",
"accession": "IGVFFI9435OMZV",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep2-BinA-PCRrep11_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T16:37:35.901961+00:00",
"file_format": "fastq",
"file_size": 5320122,
"href": "/sequence-files/IGVFFI9435OMZV/@@download/IGVFFI9435OMZV.fastq.gz",
"md5sum": "6a07b740a3fe67abd7544f497f32d6b9",
"s3_uri": "s3://igvf-files/2024/11/26/f78b6a7e-52c5-41dc-9a95-6f75cbc0f1d8/IGVFFI9435OMZV.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240426S024-Enhancer-THP1-PPIF_Enhancer_val_guides-Amp_PPIF_enhancer-BioRep1-FFrep2-BinA-PCRrep11_S473_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6700IZYS/",
"accession": "IGVFFI6700IZYS",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep2-BinA-PCRrep3_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T16:18:04.243493+00:00",
"file_format": "fastq",
"file_size": 5990704,
"href": "/sequence-files/IGVFFI6700IZYS/@@download/IGVFFI6700IZYS.fastq.gz",
"md5sum": "b4c22e6c3d0002433dddc6d41fb0c907",
"s3_uri": "s3://igvf-files/2024/11/26/4fe035ca-cf77-415e-8591-955921bfabd0/IGVFFI6700IZYS.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240426S024-Enhancer-THP1-PPIF_Enhancer_val_guides-Amp_PPIF_enhancer-BioRep1-FFrep2-BinA-PCRrep3_S465_I2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4833ZRTZ/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"notes": "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"
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7478MTAF/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7478MTAF",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep2-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": "preview",
"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": "preview",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2024-11-26T06:25:15.129639+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": "570f7eb3-724c-4cae-9ded-d4932102dbf2"
}