{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3973IRIQ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3973IRIQ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinF_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 [IGVFSM1501NWZH](/in-vitro-systems/IGVFSM1501NWZH/) 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/IGVFSM1501NWZH/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS3973IRIQ](/measurement-sets/IGVFDS3973IRIQ/) has sequence file(s) [IGVFFI8482PXCF](/sequence-files/IGVFFI8482PXCF/), [IGVFFI7236AGHI](/sequence-files/IGVFFI7236AGHI/), [IGVFFI0324TANC](/sequence-files/IGVFFI0324TANC/), [IGVFFI0596IMRN](/sequence-files/IGVFFI0596IMRN/), [IGVFFI9393FZBB](/sequence-files/IGVFFI9393FZBB/), [IGVFFI4392QMAW](/sequence-files/IGVFFI4392QMAW/), [IGVFFI2813IASO](/sequence-files/IGVFFI2813IASO/), [IGVFFI5015ZKJO](/sequence-files/IGVFFI5015ZKJO/) 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/IGVFDS3973IRIQ/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS3973IRIQ](/measurement-sets/IGVFDS3973IRIQ/) has sequence file(s): [IGVFFI8482PXCF](/sequence-files/IGVFFI8482PXCF/), [IGVFFI7236AGHI](/sequence-files/IGVFFI7236AGHI/), [IGVFFI0324TANC](/sequence-files/IGVFFI0324TANC/), [IGVFFI0596IMRN](/sequence-files/IGVFFI0596IMRN/), [IGVFFI9393FZBB](/sequence-files/IGVFFI9393FZBB/), [IGVFFI4392QMAW](/sequence-files/IGVFFI4392QMAW/), [IGVFFI2813IASO](/sequence-files/IGVFFI2813IASO/), [IGVFFI5015ZKJO](/sequence-files/IGVFFI5015ZKJO/) 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/IGVFDS3973IRIQ/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS3973IRIQ](/measurement-sets/IGVFDS3973IRIQ/) 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/IGVFDS3973IRIQ/"
}
]
},
"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": "2023-11-30T22:47:14.029891+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/IGVFFI8482PXCF/",
"accession": "IGVFFI8482PXCF",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinF-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:07:23.719732+00:00",
"file_format": "fastq",
"file_size": 3243268,
"href": "/sequence-files/IGVFFI8482PXCF/@@download/IGVFFI8482PXCF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/63d3e29d-aae4-406d-8bd6-3e17a7dbb4aa/IGVFFI8482PXCF.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-BinF-PCRrep1_S13_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7236AGHI/",
"accession": "IGVFFI7236AGHI",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinF-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:47:57.288778+00:00",
"file_format": "fastq",
"file_size": 7729173,
"href": "/sequence-files/IGVFFI7236AGHI/@@download/IGVFFI7236AGHI.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/16095d48-b459-4739-add3-6aa168e47573/IGVFFI7236AGHI.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-BinF-PCRrep2_S69_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0324TANC/",
"accession": "IGVFFI0324TANC",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinF-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:19:53.572879+00:00",
"file_format": "fastq",
"file_size": 3012652,
"href": "/sequence-files/IGVFFI0324TANC/@@download/IGVFFI0324TANC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/0597c43a-ef06-44d4-ba09-c65b06604cbc/IGVFFI0324TANC.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-BinF-PCRrep1_S13_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0596IMRN/",
"accession": "IGVFFI0596IMRN",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinF-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:00:56.996763+00:00",
"file_format": "fastq",
"file_size": 14258464,
"href": "/sequence-files/IGVFFI0596IMRN/@@download/IGVFFI0596IMRN.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/07c65c4c-42fa-4aa4-acb8-d2197c60bebf/IGVFFI0596IMRN.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-BinF-PCRrep2_S69_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9393FZBB/",
"accession": "IGVFFI9393FZBB",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinF-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:13:38.368771+00:00",
"file_format": "fastq",
"file_size": 3526947,
"href": "/sequence-files/IGVFFI9393FZBB/@@download/IGVFFI9393FZBB.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/f5673fb4-c819-494e-85a7-ca50446a3611/IGVFFI9393FZBB.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-BinF-PCRrep2_S69_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4392QMAW/",
"accession": "IGVFFI4392QMAW",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinF-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:26:14.548877+00:00",
"file_format": "fastq",
"file_size": 3202078,
"href": "/sequence-files/IGVFFI4392QMAW/@@download/IGVFFI4392QMAW.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/4aaf0acd-e8bf-4198-a346-7b2d6c05a2a0/IGVFFI4392QMAW.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-BinF-PCRrep2_S69_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2813IASO/",
"accession": "IGVFFI2813IASO",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinF-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:41:38.869205+00:00",
"file_format": "fastq",
"file_size": 7325954,
"href": "/sequence-files/IGVFFI2813IASO/@@download/IGVFFI2813IASO.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/71552a42-4528-4ca8-9f1e-abf34b839995/IGVFFI2813IASO.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-BinF-PCRrep1_S13_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5015ZKJO/",
"accession": "IGVFFI5015ZKJO",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinF-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:54:19.864442+00:00",
"file_format": "fastq",
"file_size": 13487301,
"href": "/sequence-files/IGVFFI5015ZKJO/@@download/IGVFFI5015ZKJO.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/17915310-e43f-4d56-ab6d-d290ff662346/IGVFFI5015ZKJO.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-BinF-PCRrep1_S13_R2_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": "2023-12-20T23:10:23.163351+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1501NWZH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1501NWZH",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinF"
],
"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 90-100% 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": "2023-12-05T18:41:38.869205+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": "b4d053eb-2eb1-423a-996e-e9b12ab8a78d"
}