{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1826IERV/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1826IERV",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinF_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 [IGVFDS1826IERV](/measurement-sets/IGVFDS1826IERV/) has sequence file(s) [IGVFFI0760LZKM](/sequence-files/IGVFFI0760LZKM/), [IGVFFI2485KPGY](/sequence-files/IGVFFI2485KPGY/), [IGVFFI7534VHME](/sequence-files/IGVFFI7534VHME/), [IGVFFI8033GLXS](/sequence-files/IGVFFI8033GLXS/), [IGVFFI1637KGDZ](/sequence-files/IGVFFI1637KGDZ/), [IGVFFI7385RUIE](/sequence-files/IGVFFI7385RUIE/), [IGVFFI4889NMAO](/sequence-files/IGVFFI4889NMAO/), [IGVFFI8432CQFG](/sequence-files/IGVFFI8432CQFG/) 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/IGVFDS1826IERV/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS1826IERV](/measurement-sets/IGVFDS1826IERV/) has sequence file(s): [IGVFFI0760LZKM](/sequence-files/IGVFFI0760LZKM/), [IGVFFI2485KPGY](/sequence-files/IGVFFI2485KPGY/), [IGVFFI7534VHME](/sequence-files/IGVFFI7534VHME/), [IGVFFI8033GLXS](/sequence-files/IGVFFI8033GLXS/), [IGVFFI1637KGDZ](/sequence-files/IGVFFI1637KGDZ/), [IGVFFI7385RUIE](/sequence-files/IGVFFI7385RUIE/), [IGVFFI4889NMAO](/sequence-files/IGVFFI4889NMAO/), [IGVFFI8432CQFG](/sequence-files/IGVFFI8432CQFG/) 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/IGVFDS1826IERV/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM3950QZDP](/in-vitro-systems/IGVFSM3950QZDP/) 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/IGVFSM3950QZDP/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS1826IERV](/measurement-sets/IGVFDS1826IERV/) 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/IGVFDS1826IERV/"
}
]
},
"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": "2023-12-01T00:02:56.995256+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/IGVFFI0760LZKM/",
"accession": "IGVFFI0760LZKM",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinF-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:12:37.152578+00:00",
"file_format": "fastq",
"file_size": 3321360,
"href": "/sequence-files/IGVFFI0760LZKM/@@download/IGVFFI0760LZKM.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/1f3f4aba-3e59-4434-8d7d-3ed140da5f4d/IGVFFI0760LZKM.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_S2-BioRep1-FFRep1-BinF-PCRrep2_S62_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2485KPGY/",
"accession": "IGVFFI2485KPGY",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinF-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:46:55.777627+00:00",
"file_format": "fastq",
"file_size": 7659019,
"href": "/sequence-files/IGVFFI2485KPGY/@@download/IGVFFI2485KPGY.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/70b3f9ae-8358-4bb6-aca2-9b6f4bff055a/IGVFFI2485KPGY.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_S2-BioRep1-FFRep1-BinF-PCRrep2_S62_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7534VHME/",
"accession": "IGVFFI7534VHME",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinF-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:59:48.356462+00:00",
"file_format": "fastq",
"file_size": 14107259,
"href": "/sequence-files/IGVFFI7534VHME/@@download/IGVFFI7534VHME.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/cdcf80e6-e557-4b35-ac52-8ca7036bb153/IGVFFI7534VHME.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_S2-BioRep1-FFRep1-BinF-PCRrep2_S62_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8033GLXS/",
"accession": "IGVFFI8033GLXS",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinF-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:18:52.049768+00:00",
"file_format": "fastq",
"file_size": 3268344,
"href": "/sequence-files/IGVFFI8033GLXS/@@download/IGVFFI8033GLXS.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/875936bb-91d5-4298-9dec-43c7a30ee3b9/IGVFFI8033GLXS.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_S2-BioRep1-FFRep1-BinF-PCRrep1_S6_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1637KGDZ/",
"accession": "IGVFFI1637KGDZ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinF-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:06:23.666764+00:00",
"file_format": "fastq",
"file_size": 3275018,
"href": "/sequence-files/IGVFFI1637KGDZ/@@download/IGVFFI1637KGDZ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/49e0d33e-b88e-4415-a34b-1cd04e194817/IGVFFI1637KGDZ.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_S2-BioRep1-FFRep1-BinF-PCRrep1_S6_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7385RUIE/",
"accession": "IGVFFI7385RUIE",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinF-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:40:37.288535+00:00",
"file_format": "fastq",
"file_size": 7927101,
"href": "/sequence-files/IGVFFI7385RUIE/@@download/IGVFFI7385RUIE.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/b48d8e1a-700d-4064-83d7-47ffbea7969f/IGVFFI7385RUIE.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_S2-BioRep1-FFRep1-BinF-PCRrep1_S6_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4889NMAO/",
"accession": "IGVFFI4889NMAO",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinF-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:53:15.772569+00:00",
"file_format": "fastq",
"file_size": 14594238,
"href": "/sequence-files/IGVFFI4889NMAO/@@download/IGVFFI4889NMAO.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/0d14ec96-7a88-46b5-9e9c-069bf7de8583/IGVFFI4889NMAO.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_S2-BioRep1-FFRep1-BinF-PCRrep1_S6_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8432CQFG/",
"accession": "IGVFFI8432CQFG",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinF-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:25:13.204749+00:00",
"file_format": "fastq",
"file_size": 3172655,
"href": "/sequence-files/IGVFFI8432CQFG/@@download/IGVFFI8432CQFG.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/474c4dee-9048-4e7b-889f-a0876520735f/IGVFFI8432CQFG.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_S2-BioRep1-FFRep1-BinF-PCRrep2_S62_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": "2023-12-20T23:04:28.214579+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3950QZDP/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3950QZDP",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinF"
],
"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 90-100% 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": "2023-12-05T18:40:37.288535+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": "bf45952e-f39e-40f8-bce2-a20d82462a3a"
}