{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4103BJLT/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4103BJLT",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-THP1-PE2_Exp4_NegControl_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 [IGVFDS4103BJLT](/measurement-sets/IGVFDS4103BJLT/) has sequence file(s) [IGVFFI4390SQSY](/sequence-files/IGVFFI4390SQSY/), [IGVFFI6177TTWA](/sequence-files/IGVFFI6177TTWA/), [IGVFFI5098DQLV](/sequence-files/IGVFFI5098DQLV/), [IGVFFI9896DZYL](/sequence-files/IGVFFI9896DZYL/), [IGVFFI4942LDZO](/sequence-files/IGVFFI4942LDZO/), [IGVFFI6177PIUC](/sequence-files/IGVFFI6177PIUC/), [IGVFFI3600XXOJ](/sequence-files/IGVFFI3600XXOJ/), [IGVFFI7425BWDK](/sequence-files/IGVFFI7425BWDK/) 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/IGVFDS4103BJLT/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS4103BJLT](/measurement-sets/IGVFDS4103BJLT/) has sequence file(s): [IGVFFI4390SQSY](/sequence-files/IGVFFI4390SQSY/), [IGVFFI6177TTWA](/sequence-files/IGVFFI6177TTWA/), [IGVFFI5098DQLV](/sequence-files/IGVFFI5098DQLV/), [IGVFFI9896DZYL](/sequence-files/IGVFFI9896DZYL/), [IGVFFI4942LDZO](/sequence-files/IGVFFI4942LDZO/), [IGVFFI6177PIUC](/sequence-files/IGVFFI6177PIUC/), [IGVFFI3600XXOJ](/sequence-files/IGVFFI3600XXOJ/), [IGVFFI7425BWDK](/sequence-files/IGVFFI7425BWDK/) 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/IGVFDS4103BJLT/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS4103BJLT](/measurement-sets/IGVFDS4103BJLT/) 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/IGVFDS4103BJLT/"
}
]
},
"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_for": [
{
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"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep2-BinC_AmpliconSequencing"
],
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS7922GOJN/",
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],
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS9127RZLI/",
"accession": "IGVFDS9127RZLI",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep1-BinC_AmpliconSequencing"
],
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS1319XVLL/",
"accession": "IGVFDS1319XVLL",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep2-BinA_AmpliconSequencing"
],
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS9309HKUH/",
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],
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS7312BCBZ/",
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],
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS7723OVPC/",
"accession": "IGVFDS7723OVPC",
"aliases": [
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],
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS5266OEKB/",
"accession": "IGVFDS5266OEKB",
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],
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS5752WCRU/",
"accession": "IGVFDS5752WCRU",
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],
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS0241SXOC/",
"accession": "IGVFDS0241SXOC",
"aliases": [
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],
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS5968XLTS/",
"accession": "IGVFDS5968XLTS",
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],
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},
{
"@id": "/measurement-sets/IGVFDS5468AKZL/",
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],
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},
{
"@id": "/measurement-sets/IGVFDS7736MBPH/",
"accession": "IGVFDS7736MBPH",
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],
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},
{
"@id": "/measurement-sets/IGVFDS1090HOMT/",
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],
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},
{
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{
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],
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS8230NTUC/",
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],
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},
{
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{
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],
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{
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],
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},
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},
{
"@id": "/sequence-files/IGVFFI6177PIUC/",
"accession": "IGVFFI6177PIUC",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-THP1-PE2_Exp4_NegControl-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T11:52:25.950285+00:00",
"file_format": "fastq",
"file_size": 4006646,
"href": "/sequence-files/IGVFFI6177PIUC/@@download/IGVFFI6177PIUC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/3547466f-db08-493a-b948-0fb90ecb26e4/IGVFFI6177PIUC.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240426S024-Enhancer-THP1-PPIF_Enhancer_val_guides-Amp_PPIF_enhancer-BioRep1-FFrep1-BinNeg-PCRrep2_S816_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3600XXOJ/",
"accession": "IGVFFI3600XXOJ",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-THP1-PE2_Exp4_NegControl-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T15:43:55.199081+00:00",
"file_format": "fastq",
"file_size": 4547465,
"href": "/sequence-files/IGVFFI3600XXOJ/@@download/IGVFFI3600XXOJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/ad7f8174-b352-4a7f-b7cf-760d80ff215a/IGVFFI3600XXOJ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240426S024-Enhancer-THP1-PPIF_Enhancer_val_guides-Amp_PPIF_enhancer-BioRep1-FFrep1-BinNeg-PCRrep1_S807_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7425BWDK/",
"accession": "IGVFFI7425BWDK",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-THP1-PE2_Exp4_NegControl-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T15:47:23.064671+00:00",
"file_format": "fastq",
"file_size": 4062814,
"href": "/sequence-files/IGVFFI7425BWDK/@@download/IGVFFI7425BWDK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/0cb5f989-cdaa-4c6d-9418-4f4cd9dac942/IGVFFI7425BWDK.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240426S024-Enhancer-THP1-PPIF_Enhancer_val_guides-Amp_PPIF_enhancer-BioRep1-FFrep1-BinNeg-PCRrep2_S816_I2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4833ZRTZ/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"notes": "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"
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM6087TFXW/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6087TFXW",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-THP1-PE2_Exp4_NegControl"
],
"classifications": [
"cell line"
],
"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"modality": "prime editing",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:THP-1"
],
"status": "released",
"summary": "THP-1",
"term_name": "THP-1"
}
],
"status": "preview",
"summary": "THP-1 cell line, male, Homo sapiens modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2)",
"taxa": "Homo sapiens"
}
],
"schema_version": "23",
"status": "preview",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2024-11-26T06:11:17.241145+00:00",
"summary": "prime editing Variant-EFFECTS",
"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": "93c0cf73-9901-40ad-bc7b-70e00f79fd87"
}