{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1148VATA/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1148VATA",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-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": "missing sequencing kit",
"detail": "Measurement set [IGVFDS1148VATA](/measurement-sets/IGVFDS1148VATA/) has sequence file(s) [IGVFFI7300TYRN](/sequence-files/IGVFFI7300TYRN/), [IGVFFI3126XPAX](/sequence-files/IGVFFI3126XPAX/), [IGVFFI8292WWLD](/sequence-files/IGVFFI8292WWLD/), [IGVFFI4753GHLV](/sequence-files/IGVFFI4753GHLV/), [IGVFFI4819VKVW](/sequence-files/IGVFFI4819VKVW/), [IGVFFI9242WZXT](/sequence-files/IGVFFI9242WZXT/), [IGVFFI0165WLIX](/sequence-files/IGVFFI0165WLIX/), [IGVFFI0718NYUV](/sequence-files/IGVFFI0718NYUV/) 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/IGVFDS1148VATA/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS1148VATA](/measurement-sets/IGVFDS1148VATA/) has sequence file(s): [IGVFFI7300TYRN](/sequence-files/IGVFFI7300TYRN/), [IGVFFI3126XPAX](/sequence-files/IGVFFI3126XPAX/), [IGVFFI8292WWLD](/sequence-files/IGVFFI8292WWLD/), [IGVFFI4753GHLV](/sequence-files/IGVFFI4753GHLV/), [IGVFFI4819VKVW](/sequence-files/IGVFFI4819VKVW/), [IGVFFI9242WZXT](/sequence-files/IGVFFI9242WZXT/), [IGVFFI0165WLIX](/sequence-files/IGVFFI0165WLIX/), [IGVFFI0718NYUV](/sequence-files/IGVFFI0718NYUV/) 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/IGVFDS1148VATA/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM5973PPPC](/in-vitro-systems/IGVFSM5973PPPC/) 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/IGVFSM5973PPPC/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS1148VATA](/measurement-sets/IGVFDS1148VATA/) 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/IGVFDS1148VATA/"
}
]
},
"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": "2023-11-30T22:47:18.282391+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/IGVFFI7300TYRN/",
"accession": "IGVFFI7300TYRN",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinC-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:26:49.251896+00:00",
"file_format": "fastq",
"file_size": 3061883,
"href": "/sequence-files/IGVFFI7300TYRN/@@download/IGVFFI7300TYRN.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/7e742099-7425-4311-b640-bb533e910498/IGVFFI7300TYRN.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_S5-BioRep2-FFRep1-BinC-PCRrep2_S73_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3126XPAX/",
"accession": "IGVFFI3126XPAX",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinC-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:54:56.233523+00:00",
"file_format": "fastq",
"file_size": 13058608,
"href": "/sequence-files/IGVFFI3126XPAX/@@download/IGVFFI3126XPAX.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/20022eea-9163-418a-8b55-69621f6d2179/IGVFFI3126XPAX.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_S5-BioRep2-FFRep1-BinC-PCRrep1_S17_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8292WWLD/",
"accession": "IGVFFI8292WWLD",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinC-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:14:13.123488+00:00",
"file_format": "fastq",
"file_size": 3175775,
"href": "/sequence-files/IGVFFI8292WWLD/@@download/IGVFFI8292WWLD.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/b465d948-ead1-403c-b0f4-47f0f3013d5e/IGVFFI8292WWLD.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_S5-BioRep2-FFRep1-BinC-PCRrep2_S73_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4753GHLV/",
"accession": "IGVFFI4753GHLV",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinC-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:48:32.561425+00:00",
"file_format": "fastq",
"file_size": 7513208,
"href": "/sequence-files/IGVFFI4753GHLV/@@download/IGVFFI4753GHLV.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/ebf648d6-476a-43e4-a7fe-3e629faa2185/IGVFFI4753GHLV.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_S5-BioRep2-FFRep1-BinC-PCRrep2_S73_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4819VKVW/",
"accession": "IGVFFI4819VKVW",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinC-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:07:57.804245+00:00",
"file_format": "fastq",
"file_size": 2955106,
"href": "/sequence-files/IGVFFI4819VKVW/@@download/IGVFFI4819VKVW.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/31ca524b-3715-4107-9dab-55a02a30da98/IGVFFI4819VKVW.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_S5-BioRep2-FFRep1-BinC-PCRrep1_S17_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9242WZXT/",
"accession": "IGVFFI9242WZXT",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinC-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:20:28.444795+00:00",
"file_format": "fastq",
"file_size": 2933743,
"href": "/sequence-files/IGVFFI9242WZXT/@@download/IGVFFI9242WZXT.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/c304f93c-b06c-44b7-a2a1-4eee258fd00c/IGVFFI9242WZXT.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_S5-BioRep2-FFRep1-BinC-PCRrep1_S17_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0165WLIX/",
"accession": "IGVFFI0165WLIX",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinC-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:42:14.110014+00:00",
"file_format": "fastq",
"file_size": 7121436,
"href": "/sequence-files/IGVFFI0165WLIX/@@download/IGVFFI0165WLIX.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/99e5a83d-d4fc-40b1-bd26-4d099dd73988/IGVFFI0165WLIX.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_S5-BioRep2-FFRep1-BinC-PCRrep1_S17_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0718NYUV/",
"accession": "IGVFFI0718NYUV",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinC-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:01:33.848165+00:00",
"file_format": "fastq",
"file_size": 13738734,
"href": "/sequence-files/IGVFFI0718NYUV/@@download/IGVFFI0718NYUV.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/1f24126d-1c0c-4c62-8eb8-2709934839df/IGVFFI0718NYUV.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_S5-BioRep2-FFRep1-BinC-PCRrep2_S73_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": "2023-12-20T23:10:30.799783+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5973PPPC/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5973PPPC",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-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": "2023-12-05T18:42:14.110014+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": "39730732-7440-4f58-8f36-b0d2516d9dbe"
}