{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6157FJTW/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6157FJTW",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinC_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 [IGVFSM3227FAOQ](/in-vitro-systems/IGVFSM3227FAOQ/) 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/IGVFSM3227FAOQ/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS6157FJTW](/measurement-sets/IGVFDS6157FJTW/) has sequence file(s) [IGVFFI2685VBFM](/sequence-files/IGVFFI2685VBFM/), [IGVFFI4334WLPD](/sequence-files/IGVFFI4334WLPD/), [IGVFFI9806YXLB](/sequence-files/IGVFFI9806YXLB/), [IGVFFI3307JFYO](/sequence-files/IGVFFI3307JFYO/), [IGVFFI6514PWJB](/sequence-files/IGVFFI6514PWJB/), [IGVFFI6957ZWLL](/sequence-files/IGVFFI6957ZWLL/), [IGVFFI4743VASL](/sequence-files/IGVFFI4743VASL/), [IGVFFI3015XHHH](/sequence-files/IGVFFI3015XHHH/) 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/IGVFDS6157FJTW/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS6157FJTW](/measurement-sets/IGVFDS6157FJTW/) has sequence file(s): [IGVFFI2685VBFM](/sequence-files/IGVFFI2685VBFM/), [IGVFFI4334WLPD](/sequence-files/IGVFFI4334WLPD/), [IGVFFI9806YXLB](/sequence-files/IGVFFI9806YXLB/), [IGVFFI3307JFYO](/sequence-files/IGVFFI3307JFYO/), [IGVFFI6514PWJB](/sequence-files/IGVFFI6514PWJB/), [IGVFFI6957ZWLL](/sequence-files/IGVFFI6957ZWLL/), [IGVFFI4743VASL](/sequence-files/IGVFFI4743VASL/), [IGVFFI3015XHHH](/sequence-files/IGVFFI3015XHHH/) 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/IGVFDS6157FJTW/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS6157FJTW](/measurement-sets/IGVFDS6157FJTW/) 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/IGVFDS6157FJTW/"
}
]
},
"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": "2023-11-30T22:47:25.825541+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": [
{
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"accession": "IGVFFI2685VBFM",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinC-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:43:15.331593+00:00",
"file_format": "fastq",
"file_size": 7883888,
"href": "/sequence-files/IGVFFI2685VBFM/@@download/IGVFFI2685VBFM.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/37ec5ea9-0a65-4ead-b6d2-3160fbb8a032/IGVFFI2685VBFM.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-BinC-PCRrep1_S24_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4334WLPD/",
"accession": "IGVFFI4334WLPD",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinC-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:27:50.049594+00:00",
"file_format": "fastq",
"file_size": 3257142,
"href": "/sequence-files/IGVFFI4334WLPD/@@download/IGVFFI4334WLPD.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/6c40acde-1a7b-4f97-a5ce-54a71ae514e5/IGVFFI4334WLPD.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-BinC-PCRrep2_S80_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9806YXLB/",
"accession": "IGVFFI9806YXLB",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinC-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:15:14.487292+00:00",
"file_format": "fastq",
"file_size": 3332676,
"href": "/sequence-files/IGVFFI9806YXLB/@@download/IGVFFI9806YXLB.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/b8895613-27b1-491c-937d-d3537358a4f3/IGVFFI9806YXLB.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-BinC-PCRrep2_S80_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3307JFYO/",
"accession": "IGVFFI3307JFYO",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinC-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:55:59.612397+00:00",
"file_format": "fastq",
"file_size": 14400328,
"href": "/sequence-files/IGVFFI3307JFYO/@@download/IGVFFI3307JFYO.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/2519401b-40dd-4bd7-aced-578a83f38265/IGVFFI3307JFYO.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-BinC-PCRrep1_S24_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6514PWJB/",
"accession": "IGVFFI6514PWJB",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinC-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:08:59.068711+00:00",
"file_format": "fastq",
"file_size": 3269498,
"href": "/sequence-files/IGVFFI6514PWJB/@@download/IGVFFI6514PWJB.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/a87e6656-341c-43f9-afb2-68f52306cf02/IGVFFI6514PWJB.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_S6-BioRep2-FFRep2-BinC-PCRrep1_S24_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6957ZWLL/",
"accession": "IGVFFI6957ZWLL",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinC-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:02:37.514426+00:00",
"file_format": "fastq",
"file_size": 14641255,
"href": "/sequence-files/IGVFFI6957ZWLL/@@download/IGVFFI6957ZWLL.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/38f43bcb-ae4d-42e5-866e-f5b1d7de51af/IGVFFI6957ZWLL.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-BinC-PCRrep2_S80_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4743VASL/",
"accession": "IGVFFI4743VASL",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinC-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:21:30.901471+00:00",
"file_format": "fastq",
"file_size": 3225836,
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"s3_uri": "s3://igvf-files/2023/12/05/f88e76c2-5e43-4067-bfd9-f9b5c80b4677/IGVFFI4743VASL.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_S6-BioRep2-FFRep2-BinC-PCRrep1_S24_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3015XHHH/",
"accession": "IGVFFI3015XHHH",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinC-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:49:34.131820+00:00",
"file_format": "fastq",
"file_size": 7968792,
"href": "/sequence-files/IGVFFI3015XHHH/@@download/IGVFFI3015XHHH.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/076ac40f-6c28-496e-ad01-34349c8d92f6/IGVFFI3015XHHH.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_S6-BioRep2-FFRep2-BinC-PCRrep2_S80_R1_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": "2023-12-20T23:04:43.402943+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3227FAOQ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3227FAOQ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-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": "2023-12-05T18:43:15.331593+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": "3170c5be-527e-47e8-adab-5c3517b291e6"
}