{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4045IKYV/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4045IKYV",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-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 [IGVFDS4045IKYV](/measurement-sets/IGVFDS4045IKYV/) has sequence file(s) [IGVFFI2062MCQD](/sequence-files/IGVFFI2062MCQD/), [IGVFFI7987XCSU](/sequence-files/IGVFFI7987XCSU/), [IGVFFI3386NGAV](/sequence-files/IGVFFI3386NGAV/), [IGVFFI3911BOZA](/sequence-files/IGVFFI3911BOZA/), [IGVFFI0496AFEZ](/sequence-files/IGVFFI0496AFEZ/), [IGVFFI2267STUG](/sequence-files/IGVFFI2267STUG/), [IGVFFI6287GCAB](/sequence-files/IGVFFI6287GCAB/), [IGVFFI5328UCLM](/sequence-files/IGVFFI5328UCLM/) 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/IGVFDS4045IKYV/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS4045IKYV](/measurement-sets/IGVFDS4045IKYV/) has sequence file(s): [IGVFFI2062MCQD](/sequence-files/IGVFFI2062MCQD/), [IGVFFI7987XCSU](/sequence-files/IGVFFI7987XCSU/), [IGVFFI3386NGAV](/sequence-files/IGVFFI3386NGAV/), [IGVFFI3911BOZA](/sequence-files/IGVFFI3911BOZA/), [IGVFFI0496AFEZ](/sequence-files/IGVFFI0496AFEZ/), [IGVFFI2267STUG](/sequence-files/IGVFFI2267STUG/), [IGVFFI6287GCAB](/sequence-files/IGVFFI6287GCAB/), [IGVFFI5328UCLM](/sequence-files/IGVFFI5328UCLM/) 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/IGVFDS4045IKYV/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM4346FXFH](/in-vitro-systems/IGVFSM4346FXFH/) 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/IGVFSM4346FXFH/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS4045IKYV](/measurement-sets/IGVFDS4045IKYV/) 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/IGVFDS4045IKYV/"
}
]
},
"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": "2023-11-30T22:47:10.489272+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/IGVFFI2062MCQD/",
"accession": "IGVFFI2062MCQD",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinB-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:41:03.777075+00:00",
"file_format": "fastq",
"file_size": 6994911,
"href": "/sequence-files/IGVFFI2062MCQD/@@download/IGVFFI2062MCQD.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/34f27444-cd0d-4013-bf76-64036beac03a/IGVFFI2062MCQD.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_S3-BioRep1-FFRep2-BinB-PCRrep1_S9_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7987XCSU/",
"accession": "IGVFFI7987XCSU",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinB-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:19:19.044441+00:00",
"file_format": "fastq",
"file_size": 2884656,
"href": "/sequence-files/IGVFFI7987XCSU/@@download/IGVFFI7987XCSU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/2f210741-99b8-437b-9a7f-fc0aac6b62d4/IGVFFI7987XCSU.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_S3-BioRep1-FFRep2-BinB-PCRrep1_S9_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3386NGAV/",
"accession": "IGVFFI3386NGAV",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinB-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:53:43.403787+00:00",
"file_format": "fastq",
"file_size": 12833643,
"href": "/sequence-files/IGVFFI3386NGAV/@@download/IGVFFI3386NGAV.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/a4b07ee4-5609-4b17-86b6-36ecc354b425/IGVFFI3386NGAV.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_S3-BioRep1-FFRep2-BinB-PCRrep1_S9_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3911BOZA/",
"accession": "IGVFFI3911BOZA",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinB-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:47:22.059932+00:00",
"file_format": "fastq",
"file_size": 7264631,
"href": "/sequence-files/IGVFFI3911BOZA/@@download/IGVFFI3911BOZA.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/14ed3dc8-a3c2-402f-957d-fe06dcd53fcf/IGVFFI3911BOZA.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_S3-BioRep1-FFRep2-BinB-PCRrep2_S65_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0496AFEZ/",
"accession": "IGVFFI0496AFEZ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinB-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:06:49.811467+00:00",
"file_format": "fastq",
"file_size": 3016014,
"href": "/sequence-files/IGVFFI0496AFEZ/@@download/IGVFFI0496AFEZ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/f7480b25-9c08-4aa4-9e3a-ac0f0680070b/IGVFFI0496AFEZ.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_S3-BioRep1-FFRep2-BinB-PCRrep1_S9_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2267STUG/",
"accession": "IGVFFI2267STUG",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinB-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:13:03.588951+00:00",
"file_format": "fastq",
"file_size": 3000093,
"href": "/sequence-files/IGVFFI2267STUG/@@download/IGVFFI2267STUG.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/42820860-9316-4c13-8367-ea465d3d8777/IGVFFI2267STUG.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_S3-BioRep1-FFRep2-BinB-PCRrep2_S65_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6287GCAB/",
"accession": "IGVFFI6287GCAB",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinB-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:25:39.554477+00:00",
"file_format": "fastq",
"file_size": 2975479,
"href": "/sequence-files/IGVFFI6287GCAB/@@download/IGVFFI6287GCAB.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/c1d327f7-3956-4ccd-bfa0-ed568eaf2324/IGVFFI6287GCAB.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_S3-BioRep1-FFRep2-BinB-PCRrep2_S65_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5328UCLM/",
"accession": "IGVFFI5328UCLM",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinB-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:00:19.470919+00:00",
"file_format": "fastq",
"file_size": 13340011,
"href": "/sequence-files/IGVFFI5328UCLM/@@download/IGVFFI5328UCLM.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/d1aac97c-017b-4b8a-bf22-aeacb34ac7fb/IGVFFI5328UCLM.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_S3-BioRep1-FFRep2-BinB-PCRrep2_S65_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": "2023-12-20T23:03:51.347094+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4346FXFH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4346FXFH",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-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": "2023-12-05T18:41:03.777075+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": "ec3789db-a9b2-4504-a49a-9ce09c20bab8"
}