{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5395SYKH/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5395SYKH",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinC_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 [IGVFSM5753RKHW](/in-vitro-systems/IGVFSM5753RKHW/) 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/IGVFSM5753RKHW/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS5395SYKH](/measurement-sets/IGVFDS5395SYKH/) has sequence file(s) [IGVFFI3581PVIL](/sequence-files/IGVFFI3581PVIL/), [IGVFFI1027GFFY](/sequence-files/IGVFFI1027GFFY/), [IGVFFI8793XRMT](/sequence-files/IGVFFI8793XRMT/), [IGVFFI9874DSVO](/sequence-files/IGVFFI9874DSVO/), [IGVFFI6970HHAF](/sequence-files/IGVFFI6970HHAF/), [IGVFFI8025VYHQ](/sequence-files/IGVFFI8025VYHQ/), [IGVFFI0719FVLP](/sequence-files/IGVFFI0719FVLP/), [IGVFFI5180NTAS](/sequence-files/IGVFFI5180NTAS/) 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/IGVFDS5395SYKH/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS5395SYKH](/measurement-sets/IGVFDS5395SYKH/) has sequence file(s): [IGVFFI3581PVIL](/sequence-files/IGVFFI3581PVIL/), [IGVFFI1027GFFY](/sequence-files/IGVFFI1027GFFY/), [IGVFFI8793XRMT](/sequence-files/IGVFFI8793XRMT/), [IGVFFI9874DSVO](/sequence-files/IGVFFI9874DSVO/), [IGVFFI6970HHAF](/sequence-files/IGVFFI6970HHAF/), [IGVFFI8025VYHQ](/sequence-files/IGVFFI8025VYHQ/), [IGVFFI0719FVLP](/sequence-files/IGVFFI0719FVLP/), [IGVFFI5180NTAS](/sequence-files/IGVFFI5180NTAS/) 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/IGVFDS5395SYKH/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS5395SYKH](/measurement-sets/IGVFDS5395SYKH/) 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/IGVFDS5395SYKH/"
}
]
},
"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": "2023-11-30T22:47:33.204022+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/IGVFFI3581PVIL/",
"accession": "IGVFFI3581PVIL",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinC-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:16:15.477439+00:00",
"file_format": "fastq",
"file_size": 3116993,
"href": "/sequence-files/IGVFFI3581PVIL/@@download/IGVFFI3581PVIL.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/e4c062f6-c23f-4447-adc0-55d5a7f172ef/IGVFFI3581PVIL.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_S7-BioRep3-FFRep1-BinC-PCRrep2_S87_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1027GFFY/",
"accession": "IGVFFI1027GFFY",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinC-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:57:04.136895+00:00",
"file_format": "fastq",
"file_size": 13058692,
"href": "/sequence-files/IGVFFI1027GFFY/@@download/IGVFFI1027GFFY.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/e39367f2-18d3-418a-a5a8-eefaad69a1af/IGVFFI1027GFFY.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_S7-BioRep3-FFRep1-BinC-PCRrep1_S31_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8793XRMT/",
"accession": "IGVFFI8793XRMT",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinC-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:44:16.652034+00:00",
"file_format": "fastq",
"file_size": 7187402,
"href": "/sequence-files/IGVFFI8793XRMT/@@download/IGVFFI8793XRMT.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/4868da02-c389-4a33-b8dc-c9a14ecffe3b/IGVFFI8793XRMT.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_S7-BioRep3-FFRep1-BinC-PCRrep1_S31_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9874DSVO/",
"accession": "IGVFFI9874DSVO",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinC-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:10:00.087804+00:00",
"file_format": "fastq",
"file_size": 3055385,
"href": "/sequence-files/IGVFFI9874DSVO/@@download/IGVFFI9874DSVO.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/08e445a2-cdb1-4371-ae2d-e80d48e245c4/IGVFFI9874DSVO.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_S7-BioRep3-FFRep1-BinC-PCRrep1_S31_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6970HHAF/",
"accession": "IGVFFI6970HHAF",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinC-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:03:41.230366+00:00",
"file_format": "fastq",
"file_size": 13833960,
"href": "/sequence-files/IGVFFI6970HHAF/@@download/IGVFFI6970HHAF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/221c3751-59aa-4da8-b4c4-8c91b3fc1bdc/IGVFFI6970HHAF.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_S7-BioRep3-FFRep1-BinC-PCRrep2_S87_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8025VYHQ/",
"accession": "IGVFFI8025VYHQ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinC-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:50:35.669938+00:00",
"file_format": "fastq",
"file_size": 7573075,
"href": "/sequence-files/IGVFFI8025VYHQ/@@download/IGVFFI8025VYHQ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/d6399efe-027a-427c-87d1-ffd21acf003a/IGVFFI8025VYHQ.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_S7-BioRep3-FFRep1-BinC-PCRrep2_S87_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0719FVLP/",
"accession": "IGVFFI0719FVLP",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinC-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:22:32.359748+00:00",
"file_format": "fastq",
"file_size": 2938056,
"href": "/sequence-files/IGVFFI0719FVLP/@@download/IGVFFI0719FVLP.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/e6f3d3d8-7c8a-4d51-9f00-67fff7ad1846/IGVFFI0719FVLP.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_S7-BioRep3-FFRep1-BinC-PCRrep1_S31_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5180NTAS/",
"accession": "IGVFFI5180NTAS",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinC-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:28:50.971205+00:00",
"file_format": "fastq",
"file_size": 3101217,
"href": "/sequence-files/IGVFFI5180NTAS/@@download/IGVFFI5180NTAS.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/e05a93f9-87ec-4927-a3a3-a2db59720b92/IGVFFI5180NTAS.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_S7-BioRep3-FFRep1-BinC-PCRrep2_S87_I2_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": "2023-12-20T23:03:57.636986+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5753RKHW/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5753RKHW",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinC"
],
"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 35-45% 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": "2023-12-05T18:44:16.652034+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": "47c611ad-b37b-48da-a026-9ac72e9be1ae"
}