{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5488ZDOV/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5488ZDOV",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinA_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 measurement set [IGVFDS5488ZDOV](/measurement-sets/IGVFDS5488ZDOV/) has deleted subobject auxiliary set [IGVFDS4840LCRI](/auxiliary-sets/IGVFDS4840LCRI/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS5488ZDOV/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM2682WCYF](/in-vitro-systems/IGVFSM2682WCYF/) 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/IGVFSM2682WCYF/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS5488ZDOV](/measurement-sets/IGVFDS5488ZDOV/) has sequence file(s) [IGVFFI9822WQUG](/sequence-files/IGVFFI9822WQUG/), [IGVFFI5933YKPN](/sequence-files/IGVFFI5933YKPN/), [IGVFFI4984HOUN](/sequence-files/IGVFFI4984HOUN/), [IGVFFI6865GPUP](/sequence-files/IGVFFI6865GPUP/), [IGVFFI9580WBYQ](/sequence-files/IGVFFI9580WBYQ/), [IGVFFI1898LDJF](/sequence-files/IGVFFI1898LDJF/), [IGVFFI7357HNVT](/sequence-files/IGVFFI7357HNVT/), [IGVFFI6083TOMF](/sequence-files/IGVFFI6083TOMF/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_inconsistent_sequencing_kit",
"path": "/measurement-sets/IGVFDS5488ZDOV/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS5488ZDOV](/measurement-sets/IGVFDS5488ZDOV/) has sequence file(s): [IGVFFI9822WQUG](/sequence-files/IGVFFI9822WQUG/), [IGVFFI5933YKPN](/sequence-files/IGVFFI5933YKPN/), [IGVFFI4984HOUN](/sequence-files/IGVFFI4984HOUN/), [IGVFFI6865GPUP](/sequence-files/IGVFFI6865GPUP/), [IGVFFI9580WBYQ](/sequence-files/IGVFFI9580WBYQ/), [IGVFFI1898LDJF](/sequence-files/IGVFFI1898LDJF/), [IGVFFI7357HNVT](/sequence-files/IGVFFI7357HNVT/), [IGVFFI6083TOMF](/sequence-files/IGVFFI6083TOMF/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS5488ZDOV/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS5488ZDOV](/measurement-sets/IGVFDS5488ZDOV/) 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": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_auxiliary_set",
"path": "/measurement-sets/IGVFDS5488ZDOV/"
}
],
"WARNING": [
{
"category": "unexpected files",
"detail": "Measurement set [IGVFDS5488ZDOV](/measurement-sets/IGVFDS5488ZDOV/) has `files`. CRISPR screen measurement sets without a scRNA-seq readout are not expected to have files.",
"level": 40,
"level_name": "WARNING",
"name": "audit_no_files",
"path": "/measurement-sets/IGVFDS5488ZDOV/"
},
{
"category": "missing files",
"detail": "Auxiliary set [IGVFDS4840LCRI](/auxiliary-sets/IGVFDS4840LCRI/) has no `files`. File sets are expected to have files.",
"level": 40,
"level_name": "WARNING",
"name": "audit_no_files",
"path": "/auxiliary-sets/IGVFDS4840LCRI/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS4840LCRI/",
"accession": "IGVFDS4840LCRI",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinA_AmpliconSequencing_AuxiliarySet"
],
"file_set_type": "variant sequencing",
"status": "deleted"
}
],
"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": "2023-11-30T22:47:08.113571+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/IGVFFI9822WQUG/",
"accession": "IGVFFI9822WQUG",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinA-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:00:10.308121+00:00",
"file_format": "fastq",
"file_size": 12708511,
"href": "/sequence-files/IGVFFI9822WQUG/@@download/IGVFFI9822WQUG.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/68e8dc93-9034-4fbc-a8ff-0ca9d3dc82cd/IGVFFI9822WQUG.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_S3-BioRep1-FFRep2-BinA-PCRrep2_S64_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5933YKPN/",
"accession": "IGVFFI5933YKPN",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinA-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:40:55.089920+00:00",
"file_format": "fastq",
"file_size": 7453662,
"href": "/sequence-files/IGVFFI5933YKPN/@@download/IGVFFI5933YKPN.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/dbada4a9-1661-40d2-8ef6-986daf4d033a/IGVFFI5933YKPN.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_S3-BioRep1-FFRep2-BinA-PCRrep1_S8_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4984HOUN/",
"accession": "IGVFFI4984HOUN",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinA-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:47:13.343482+00:00",
"file_format": "fastq",
"file_size": 6999620,
"href": "/sequence-files/IGVFFI4984HOUN/@@download/IGVFFI4984HOUN.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/39297619-5c67-4fe0-ad95-c0c98ce3fe86/IGVFFI4984HOUN.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_S3-BioRep1-FFRep2-BinA-PCRrep2_S64_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6865GPUP/",
"accession": "IGVFFI6865GPUP",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinA-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:19:10.365935+00:00",
"file_format": "fastq",
"file_size": 3046923,
"href": "/sequence-files/IGVFFI6865GPUP/@@download/IGVFFI6865GPUP.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/c235060b-9de3-4a01-bd70-dfe343485c60/IGVFFI6865GPUP.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_S3-BioRep1-FFRep2-BinA-PCRrep1_S8_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9580WBYQ/",
"accession": "IGVFFI9580WBYQ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinA-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:53:33.942943+00:00",
"file_format": "fastq",
"file_size": 13646489,
"href": "/sequence-files/IGVFFI9580WBYQ/@@download/IGVFFI9580WBYQ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/0f021a1d-b231-41d4-b50c-767e40d95e1b/IGVFFI9580WBYQ.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_S3-BioRep1-FFRep2-BinA-PCRrep1_S8_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1898LDJF/",
"accession": "IGVFFI1898LDJF",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinA-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:25:30.797987+00:00",
"file_format": "fastq",
"file_size": 2835903,
"href": "/sequence-files/IGVFFI1898LDJF/@@download/IGVFFI1898LDJF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/40a99909-21bb-41d5-8ccb-074f92cf15d5/IGVFFI1898LDJF.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_S3-BioRep1-FFRep2-BinA-PCRrep2_S64_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7357HNVT/",
"accession": "IGVFFI7357HNVT",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinA-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:06:40.976536+00:00",
"file_format": "fastq",
"file_size": 3312802,
"href": "/sequence-files/IGVFFI7357HNVT/@@download/IGVFFI7357HNVT.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/9611afbf-84c5-49bd-847c-509cb2bc0336/IGVFFI7357HNVT.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_S3-BioRep1-FFRep2-BinA-PCRrep1_S8_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6083TOMF/",
"accession": "IGVFFI6083TOMF",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinA-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:12:54.699808+00:00",
"file_format": "fastq",
"file_size": 2976084,
"href": "/sequence-files/IGVFFI6083TOMF/@@download/IGVFFI6083TOMF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/5aff5eee-ff9c-46f7-bbc0-5507b8d7db14/IGVFFI6083TOMF.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_S3-BioRep1-FFRep2-BinA-PCRrep2_S64_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": "2023-12-20T23:04:57.566992+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2682WCYF/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2682WCYF",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinA"
],
"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 0-10% 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": "2023-12-05T18:40:55.089920+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": "f5e52f05-55d5-4b34-b122-b0a68b71b1d6"
}