{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5248WHUK/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5248WHUK",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinB_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 [IGVFDS5248WHUK](/measurement-sets/IGVFDS5248WHUK/) has sequence file(s) [IGVFFI8442SISZ](/sequence-files/IGVFFI8442SISZ/), [IGVFFI4022TDNY](/sequence-files/IGVFFI4022TDNY/), [IGVFFI4067RGPT](/sequence-files/IGVFFI4067RGPT/), [IGVFFI1894ZYAU](/sequence-files/IGVFFI1894ZYAU/), [IGVFFI0099VUEY](/sequence-files/IGVFFI0099VUEY/), [IGVFFI8207FOTO](/sequence-files/IGVFFI8207FOTO/), [IGVFFI1960GGRL](/sequence-files/IGVFFI1960GGRL/), [IGVFFI2710HZQA](/sequence-files/IGVFFI2710HZQA/) 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/IGVFDS5248WHUK/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS5248WHUK](/measurement-sets/IGVFDS5248WHUK/) has sequence file(s): [IGVFFI8442SISZ](/sequence-files/IGVFFI8442SISZ/), [IGVFFI4022TDNY](/sequence-files/IGVFFI4022TDNY/), [IGVFFI4067RGPT](/sequence-files/IGVFFI4067RGPT/), [IGVFFI1894ZYAU](/sequence-files/IGVFFI1894ZYAU/), [IGVFFI0099VUEY](/sequence-files/IGVFFI0099VUEY/), [IGVFFI8207FOTO](/sequence-files/IGVFFI8207FOTO/), [IGVFFI1960GGRL](/sequence-files/IGVFFI1960GGRL/), [IGVFFI2710HZQA](/sequence-files/IGVFFI2710HZQA/) 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/IGVFDS5248WHUK/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM9819UGFN](/in-vitro-systems/IGVFSM9819UGFN/) 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/IGVFSM9819UGFN/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS5248WHUK](/measurement-sets/IGVFDS5248WHUK/) 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/IGVFDS5248WHUK/"
}
]
},
"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": "2023-11-30T22:47:39.769939+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/IGVFFI8442SISZ/",
"accession": "IGVFFI8442SISZ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinB-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:57:58.496711+00:00",
"file_format": "fastq",
"file_size": 13988346,
"href": "/sequence-files/IGVFFI8442SISZ/@@download/IGVFFI8442SISZ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/5b94f2e7-375a-4e10-95a4-2e5884bb1f55/IGVFFI8442SISZ.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_S8-BioRep3-FFRep2-BinB-PCRrep1_S37_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4022TDNY/",
"accession": "IGVFFI4022TDNY",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinB-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:51:28.275088+00:00",
"file_format": "fastq",
"file_size": 7761606,
"href": "/sequence-files/IGVFFI4022TDNY/@@download/IGVFFI4022TDNY.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/dde8b73e-9d78-4e97-8c7c-853e171e2741/IGVFFI4022TDNY.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_S8-BioRep3-FFRep2-BinB-PCRrep2_S93_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4067RGPT/",
"accession": "IGVFFI4067RGPT",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinB-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:23:28.261748+00:00",
"file_format": "fastq",
"file_size": 3132951,
"href": "/sequence-files/IGVFFI4067RGPT/@@download/IGVFFI4067RGPT.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/c87f6421-06db-438a-b49e-8f5d0aa17c45/IGVFFI4067RGPT.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_S8-BioRep3-FFRep2-BinB-PCRrep1_S37_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1894ZYAU/",
"accession": "IGVFFI1894ZYAU",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinB-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:10:52.214260+00:00",
"file_format": "fastq",
"file_size": 3459403,
"href": "/sequence-files/IGVFFI1894ZYAU/@@download/IGVFFI1894ZYAU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/e27cb2fd-d290-4da5-ad0c-4e256a506d93/IGVFFI1894ZYAU.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_S8-BioRep3-FFRep2-BinB-PCRrep1_S37_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0099VUEY/",
"accession": "IGVFFI0099VUEY",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinB-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:45:10.451039+00:00",
"file_format": "fastq",
"file_size": 7722493,
"href": "/sequence-files/IGVFFI0099VUEY/@@download/IGVFFI0099VUEY.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/bed09cb2-e201-4709-9fa4-1d8c7ae474bf/IGVFFI0099VUEY.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_S8-BioRep3-FFRep2-BinB-PCRrep1_S37_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8207FOTO/",
"accession": "IGVFFI8207FOTO",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinB-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:17:07.980596+00:00",
"file_format": "fastq",
"file_size": 3246939,
"href": "/sequence-files/IGVFFI8207FOTO/@@download/IGVFFI8207FOTO.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/3d29e3ff-b6e9-4bae-9761-5a04601aa0b5/IGVFFI8207FOTO.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_S8-BioRep3-FFRep2-BinB-PCRrep2_S93_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1960GGRL/",
"accession": "IGVFFI1960GGRL",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinB-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:04:36.320065+00:00",
"file_format": "fastq",
"file_size": 14298794,
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"s3_uri": "s3://igvf-files/2023/12/05/f83f8fdf-54cb-4a57-9f91-344c05969855/IGVFFI1960GGRL.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_S8-BioRep3-FFRep2-BinB-PCRrep2_S93_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2710HZQA/",
"accession": "IGVFFI2710HZQA",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinB-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:29:42.956559+00:00",
"file_format": "fastq",
"file_size": 3217940,
"href": "/sequence-files/IGVFFI2710HZQA/@@download/IGVFFI2710HZQA.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/e1165195-f956-412e-b4b2-cc2edc736188/IGVFFI2710HZQA.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_S8-BioRep3-FFRep2-BinB-PCRrep2_S93_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": "2023-12-20T23:10:58.485139+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9819UGFN/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9819UGFN",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinB"
],
"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 11-20% 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": "2023-12-05T18:45:10.451039+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": "ed9c7e22-e877-4c91-894d-5d221d18270a"
}