{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1682DWUE/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1682DWUE",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-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 [IGVFDS1682DWUE](/measurement-sets/IGVFDS1682DWUE/) has sequence file(s) [IGVFFI8009JPES](/sequence-files/IGVFFI8009JPES/), [IGVFFI4604IZZB](/sequence-files/IGVFFI4604IZZB/), [IGVFFI8896AAKI](/sequence-files/IGVFFI8896AAKI/), [IGVFFI8971WOVP](/sequence-files/IGVFFI8971WOVP/), [IGVFFI6110CVQC](/sequence-files/IGVFFI6110CVQC/), [IGVFFI1170AKFE](/sequence-files/IGVFFI1170AKFE/), [IGVFFI3214YMCP](/sequence-files/IGVFFI3214YMCP/), [IGVFFI2668UBBA](/sequence-files/IGVFFI2668UBBA/) 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/IGVFDS1682DWUE/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS1682DWUE](/measurement-sets/IGVFDS1682DWUE/) has sequence file(s): [IGVFFI8009JPES](/sequence-files/IGVFFI8009JPES/), [IGVFFI4604IZZB](/sequence-files/IGVFFI4604IZZB/), [IGVFFI8896AAKI](/sequence-files/IGVFFI8896AAKI/), [IGVFFI8971WOVP](/sequence-files/IGVFFI8971WOVP/), [IGVFFI6110CVQC](/sequence-files/IGVFFI6110CVQC/), [IGVFFI1170AKFE](/sequence-files/IGVFFI1170AKFE/), [IGVFFI3214YMCP](/sequence-files/IGVFFI3214YMCP/), [IGVFFI2668UBBA](/sequence-files/IGVFFI2668UBBA/) 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/IGVFDS1682DWUE/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM4109MDZC](/in-vitro-systems/IGVFSM4109MDZC/) 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/IGVFSM4109MDZC/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS1682DWUE](/measurement-sets/IGVFDS1682DWUE/) 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/IGVFDS1682DWUE/"
}
]
},
"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": "2023-11-30T22:47:36.350545+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/IGVFFI8009JPES/",
"accession": "IGVFFI8009JPES",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinF-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:10:26.236417+00:00",
"file_format": "fastq",
"file_size": 3467839,
"href": "/sequence-files/IGVFFI8009JPES/@@download/IGVFFI8009JPES.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/5e61fa17-1684-468b-b4b4-410c51b5599f/IGVFFI8009JPES.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_S7-BioRep3-FFRep1-BinF-PCRrep1_S34_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4604IZZB/",
"accession": "IGVFFI4604IZZB",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinF-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:22:58.522380+00:00",
"file_format": "fastq",
"file_size": 3151099,
"href": "/sequence-files/IGVFFI4604IZZB/@@download/IGVFFI4604IZZB.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/8701bbdb-3346-459a-a3eb-72efaccfb0db/IGVFFI4604IZZB.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_S7-BioRep3-FFRep1-BinF-PCRrep1_S34_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8896AAKI/",
"accession": "IGVFFI8896AAKI",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinF-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:16:41.624604+00:00",
"file_format": "fastq",
"file_size": 3205025,
"href": "/sequence-files/IGVFFI8896AAKI/@@download/IGVFFI8896AAKI.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/8cff0feb-c77a-4fd8-941f-27df07e3da37/IGVFFI8896AAKI.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_S7-BioRep3-FFRep1-BinF-PCRrep2_S90_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8971WOVP/",
"accession": "IGVFFI8971WOVP",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinF-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:51:01.805064+00:00",
"file_format": "fastq",
"file_size": 7514067,
"href": "/sequence-files/IGVFFI8971WOVP/@@download/IGVFFI8971WOVP.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/dbcd1669-bbc0-4a18-8c6d-c5b944d9c895/IGVFFI8971WOVP.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_S7-BioRep3-FFRep1-BinF-PCRrep2_S90_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6110CVQC/",
"accession": "IGVFFI6110CVQC",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinF-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:44:42.797873+00:00",
"file_format": "fastq",
"file_size": 7636092,
"href": "/sequence-files/IGVFFI6110CVQC/@@download/IGVFFI6110CVQC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/2020777d-c6cc-48b1-bcf1-351588393f56/IGVFFI6110CVQC.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_S7-BioRep3-FFRep1-BinF-PCRrep1_S34_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1170AKFE/",
"accession": "IGVFFI1170AKFE",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinF-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:29:16.854234+00:00",
"file_format": "fastq",
"file_size": 3102626,
"href": "/sequence-files/IGVFFI1170AKFE/@@download/IGVFFI1170AKFE.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/a2ae01a7-abc6-4bd3-aca9-7b5749bd9a03/IGVFFI1170AKFE.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_S7-BioRep3-FFRep1-BinF-PCRrep2_S90_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3214YMCP/",
"accession": "IGVFFI3214YMCP",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinF-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:04:08.449368+00:00",
"file_format": "fastq",
"file_size": 13780663,
"href": "/sequence-files/IGVFFI3214YMCP/@@download/IGVFFI3214YMCP.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/82465df2-b787-4d87-a312-7379580f00a5/IGVFFI3214YMCP.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_S7-BioRep3-FFRep1-BinF-PCRrep2_S90_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2668UBBA/",
"accession": "IGVFFI2668UBBA",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinF-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:57:31.460706+00:00",
"file_format": "fastq",
"file_size": 14039208,
"href": "/sequence-files/IGVFFI2668UBBA/@@download/IGVFFI2668UBBA.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/c655e7a8-9ec1-4742-b0ac-cfc48936938f/IGVFFI2668UBBA.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_S7-BioRep3-FFRep1-BinF-PCRrep1_S34_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": "2023-12-20T23:04:47.406948+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4109MDZC/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4109MDZC",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-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": "2023-12-05T18:44:42.797873+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": "1de730a0-fbdc-4d7e-bf43-d7f83cf1a82c"
}