{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9366UFCD/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9366UFCD",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinD_AmpliconSequencing"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"status": "released",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM8465VLDG](/in-vitro-systems/IGVFSM8465VLDG/) has in progress subobject construct library set [IGVFDS6377KNCH](/construct-library-sets/IGVFDS6377KNCH/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM8465VLDG/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS9366UFCD](/measurement-sets/IGVFDS9366UFCD/) has sequence file(s) [IGVFFI1446FDWJ](/sequence-files/IGVFFI1446FDWJ/), [IGVFFI9506PTOQ](/sequence-files/IGVFFI9506PTOQ/), [IGVFFI9635ZZYA](/sequence-files/IGVFFI9635ZZYA/), [IGVFFI1604QEDA](/sequence-files/IGVFFI1604QEDA/), [IGVFFI6012EPQC](/sequence-files/IGVFFI6012EPQC/), [IGVFFI6284XKDH](/sequence-files/IGVFFI6284XKDH/), [IGVFFI5022RIQE](/sequence-files/IGVFFI5022RIQE/), [IGVFFI4102MAGN](/sequence-files/IGVFFI4102MAGN/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/measurement-sets/IGVFDS9366UFCD/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS9366UFCD](/measurement-sets/IGVFDS9366UFCD/) has sequence file(s): [IGVFFI1446FDWJ](/sequence-files/IGVFFI1446FDWJ/), [IGVFFI9506PTOQ](/sequence-files/IGVFFI9506PTOQ/), [IGVFFI9635ZZYA](/sequence-files/IGVFFI9635ZZYA/), [IGVFFI1604QEDA](/sequence-files/IGVFFI1604QEDA/), [IGVFFI6012EPQC](/sequence-files/IGVFFI6012EPQC/), [IGVFFI6284XKDH](/sequence-files/IGVFFI6284XKDH/), [IGVFFI5022RIQE](/sequence-files/IGVFFI5022RIQE/), [IGVFFI4102MAGN](/sequence-files/IGVFFI4102MAGN/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS9366UFCD/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS9366UFCD](/measurement-sets/IGVFDS9366UFCD/) 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/IGVFDS9366UFCD/"
}
]
},
"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"
},
"control_file_sets": [
{
"@id": "/measurement-sets/IGVFDS9477ARWI/",
"accession": "IGVFDS9477ARWI",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-Jurkat-PE2_Exp1_NegControl_AmpliconSequencing",
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-Jurkat-PE2_Exp1_NegControl_AmpliconSequencing"
],
"status": "released"
}
],
"control_for": [],
"creation_timestamp": "2023-11-30T22:47:27.241134+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO1080XFGV/",
"accession": "IGVFDO1080XFGV",
"aliases": [
"igvf:donor_of_Jurkat"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI1446FDWJ/",
"accession": "IGVFFI1446FDWJ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinD-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:27:58.689297+00:00",
"file_format": "fastq",
"file_size": 3079998,
"href": "/sequence-files/IGVFFI1446FDWJ/@@download/IGVFFI1446FDWJ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/b71ef1d5-c209-4506-8ce0-94c0628039e1/IGVFFI1446FDWJ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S6-BioRep2-FFRep2-BinD-PCRrep2_S81_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9506PTOQ/",
"accession": "IGVFFI9506PTOQ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinD-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:43:24.162524+00:00",
"file_format": "fastq",
"file_size": 7703427,
"href": "/sequence-files/IGVFFI9506PTOQ/@@download/IGVFFI9506PTOQ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/12aa39f4-37b6-4291-b4ed-169b50ee7480/IGVFFI9506PTOQ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S6-BioRep2-FFRep2-BinD-PCRrep1_S25_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9635ZZYA/",
"accession": "IGVFFI9635ZZYA",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinD-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:21:39.710203+00:00",
"file_format": "fastq",
"file_size": 3166421,
"href": "/sequence-files/IGVFFI9635ZZYA/@@download/IGVFFI9635ZZYA.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/475332e6-8c83-4d32-a1c8-8e9b61d2e4e1/IGVFFI9635ZZYA.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S6-BioRep2-FFRep2-BinD-PCRrep1_S25_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1604QEDA/",
"accession": "IGVFFI1604QEDA",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinD-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:49:42.959758+00:00",
"file_format": "fastq",
"file_size": 7510997,
"href": "/sequence-files/IGVFFI1604QEDA/@@download/IGVFFI1604QEDA.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/ac7c27ab-a49c-4e3a-88c7-c21d3352330f/IGVFFI1604QEDA.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S6-BioRep2-FFRep2-BinD-PCRrep2_S81_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6012EPQC/",
"accession": "IGVFFI6012EPQC",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinD-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:56:08.872606+00:00",
"file_format": "fastq",
"file_size": 14101995,
"href": "/sequence-files/IGVFFI6012EPQC/@@download/IGVFFI6012EPQC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/93014a38-12dd-4187-b1ee-5f5ecc1bb316/IGVFFI6012EPQC.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S6-BioRep2-FFRep2-BinD-PCRrep1_S25_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6284XKDH/",
"accession": "IGVFFI6284XKDH",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinD-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:02:46.539999+00:00",
"file_format": "fastq",
"file_size": 13754059,
"href": "/sequence-files/IGVFFI6284XKDH/@@download/IGVFFI6284XKDH.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/6deecdbb-cf33-499e-9449-6b58548fa91c/IGVFFI6284XKDH.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S6-BioRep2-FFRep2-BinD-PCRrep2_S81_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5022RIQE/",
"accession": "IGVFFI5022RIQE",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinD-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:15:23.128032+00:00",
"file_format": "fastq",
"file_size": 3143953,
"href": "/sequence-files/IGVFFI5022RIQE/@@download/IGVFFI5022RIQE.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/51e0387a-f6df-41ec-93db-e3822c659276/IGVFFI5022RIQE.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S6-BioRep2-FFRep2-BinD-PCRrep2_S81_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4102MAGN/",
"accession": "IGVFFI4102MAGN",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinD-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:09:07.886588+00:00",
"file_format": "fastq",
"file_size": 3321982,
"href": "/sequence-files/IGVFFI4102MAGN/@@download/IGVFFI4102MAGN.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/0bc3acf9-3fd4-4c2c-a62a-4952cafad175/IGVFFI4102MAGN.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S6-BioRep2-FFRep2-BinD-PCRrep1_S25_I1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS9162RHFP/"
],
"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": "2023-12-20T23:10:59.645644+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8465VLDG/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8465VLDG",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinD"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS6377KNCH/",
"accession": "IGVFDS6377KNCH",
"file_set_type": "guide library",
"status": "in progress",
"summary": "guide (sgRNA) library targeting sequence variants in a genomic locus"
}
],
"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"modality": "prime editing",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002796/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:Jurkat"
],
"status": "released",
"summary": "Jurkat",
"term_name": "Jurkat"
}
],
"status": "released",
"summary": "Jurkat cell line, male, Homo sapiens (sorting details: FACS bin for 55-65% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transfected with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "23",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T18:43:24.162524+00:00",
"summary": "CRISPR prime editing Variant-EFFECTS 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": [
"rotamase F",
"CYP3",
"cyclophilin F",
"mitochondrial cyclophilin",
"peptidyl-prolyl cis-trans isomerase, mitochondrial",
"CypD",
"Cyp-D",
"cyclophilin 3",
"cyclophilin D",
"CyP-M",
"peptidyl-prolyl cis-trans isomerase F, mitochondrial",
"PPIase F"
]
}
],
"uuid": "dce93854-a5eb-4cbf-b9b9-40052ce20895"
}