{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0563SROG/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0563SROG",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-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 in vitro system [IGVFSM0564OGQD](/in-vitro-systems/IGVFSM0564OGQD/) 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/IGVFSM0564OGQD/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS0563SROG](/measurement-sets/IGVFDS0563SROG/) has sequence file(s) [IGVFFI2095FWYA](/sequence-files/IGVFFI2095FWYA/), [IGVFFI9046IEPX](/sequence-files/IGVFFI9046IEPX/), [IGVFFI6778PRQT](/sequence-files/IGVFFI6778PRQT/), [IGVFFI3985ZGWN](/sequence-files/IGVFFI3985ZGWN/), [IGVFFI6736QGBU](/sequence-files/IGVFFI6736QGBU/), [IGVFFI5589AAFO](/sequence-files/IGVFFI5589AAFO/), [IGVFFI9538TETI](/sequence-files/IGVFFI9538TETI/), [IGVFFI1154SUGO](/sequence-files/IGVFFI1154SUGO/) 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/IGVFDS0563SROG/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS0563SROG](/measurement-sets/IGVFDS0563SROG/) has sequence file(s): [IGVFFI2095FWYA](/sequence-files/IGVFFI2095FWYA/), [IGVFFI9046IEPX](/sequence-files/IGVFFI9046IEPX/), [IGVFFI6778PRQT](/sequence-files/IGVFFI6778PRQT/), [IGVFFI3985ZGWN](/sequence-files/IGVFFI3985ZGWN/), [IGVFFI6736QGBU](/sequence-files/IGVFFI6736QGBU/), [IGVFFI5589AAFO](/sequence-files/IGVFFI5589AAFO/), [IGVFFI9538TETI](/sequence-files/IGVFFI9538TETI/), [IGVFFI1154SUGO](/sequence-files/IGVFFI1154SUGO/) 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/IGVFDS0563SROG/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS0563SROG](/measurement-sets/IGVFDS0563SROG/) 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/IGVFDS0563SROG/"
}
]
},
"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": "2023-11-30T22:47:22.273461+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/IGVFFI2095FWYA/",
"accession": "IGVFFI2095FWYA",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinA-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:14:56.869856+00:00",
"file_format": "fastq",
"file_size": 3070413,
"href": "/sequence-files/IGVFFI2095FWYA/@@download/IGVFFI2095FWYA.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/e6b5ad96-94a0-48b0-b742-c896a6cd7634/IGVFFI2095FWYA.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-BinA-PCRrep2_S78_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9046IEPX/",
"accession": "IGVFFI9046IEPX",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinA-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:27:32.263902+00:00",
"file_format": "fastq",
"file_size": 2970229,
"href": "/sequence-files/IGVFFI9046IEPX/@@download/IGVFFI9046IEPX.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/429c1de9-ab87-4268-bb95-51beb591696a/IGVFFI9046IEPX.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-BinA-PCRrep2_S78_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6778PRQT/",
"accession": "IGVFFI6778PRQT",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinA-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:02:19.408734+00:00",
"file_format": "fastq",
"file_size": 13282846,
"href": "/sequence-files/IGVFFI6778PRQT/@@download/IGVFFI6778PRQT.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/d44e30dd-8b4f-4223-bf23-95308aa90881/IGVFFI6778PRQT.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-BinA-PCRrep2_S78_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3985ZGWN/",
"accession": "IGVFFI3985ZGWN",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinA-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:42:57.904682+00:00",
"file_format": "fastq",
"file_size": 7376454,
"href": "/sequence-files/IGVFFI3985ZGWN/@@download/IGVFFI3985ZGWN.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/6fe08132-2960-42c1-9cf5-ea2d825003f5/IGVFFI3985ZGWN.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-BinA-PCRrep1_S22_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6736QGBU/",
"accession": "IGVFFI6736QGBU",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinA-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:55:41.448853+00:00",
"file_format": "fastq",
"file_size": 13451903,
"href": "/sequence-files/IGVFFI6736QGBU/@@download/IGVFFI6736QGBU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/5cc83f2a-6cdf-45fe-b36b-1a8c5e392e5e/IGVFFI6736QGBU.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-BinA-PCRrep1_S22_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5589AAFO/",
"accession": "IGVFFI5589AAFO",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinA-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:08:41.366664+00:00",
"file_format": "fastq",
"file_size": 3183553,
"href": "/sequence-files/IGVFFI5589AAFO/@@download/IGVFFI5589AAFO.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/dd1e457a-3c09-49b5-b51a-2dcb9dc05809/IGVFFI5589AAFO.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-BinA-PCRrep1_S22_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9538TETI/",
"accession": "IGVFFI9538TETI",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinA-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:49:16.583694+00:00",
"file_format": "fastq",
"file_size": 7274679,
"href": "/sequence-files/IGVFFI9538TETI/@@download/IGVFFI9538TETI.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/40e1634b-2744-45ff-8e23-d0f2fef6a076/IGVFFI9538TETI.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-BinA-PCRrep2_S78_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1154SUGO/",
"accession": "IGVFFI1154SUGO",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinA-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:21:13.448312+00:00",
"file_format": "fastq",
"file_size": 3004235,
"href": "/sequence-files/IGVFFI1154SUGO/@@download/IGVFFI1154SUGO.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/05664d7e-748e-46bb-a363-08707d203ac9/IGVFFI1154SUGO.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-BinA-PCRrep1_S22_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": "2023-12-20T23:04:20.539053+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0564OGQD/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0564OGQD",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-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": "2023-12-05T18:42:57.904682+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": "f3c63fb5-0beb-49ff-a97b-76e393bc908e"
}