{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3034JURQ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3034JURQ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-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": "missing sequencing kit",
"detail": "Measurement set [IGVFDS3034JURQ](/measurement-sets/IGVFDS3034JURQ/) has sequence file(s) [IGVFFI6538LPYR](/sequence-files/IGVFFI6538LPYR/), [IGVFFI5823XHAH](/sequence-files/IGVFFI5823XHAH/), [IGVFFI8084AYAZ](/sequence-files/IGVFFI8084AYAZ/), [IGVFFI6790GXFV](/sequence-files/IGVFFI6790GXFV/), [IGVFFI0086RCFO](/sequence-files/IGVFFI0086RCFO/), [IGVFFI7583EKHH](/sequence-files/IGVFFI7583EKHH/), [IGVFFI9229HMQG](/sequence-files/IGVFFI9229HMQG/), [IGVFFI6472EHNR](/sequence-files/IGVFFI6472EHNR/) 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/IGVFDS3034JURQ/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS3034JURQ](/measurement-sets/IGVFDS3034JURQ/) has sequence file(s): [IGVFFI6538LPYR](/sequence-files/IGVFFI6538LPYR/), [IGVFFI5823XHAH](/sequence-files/IGVFFI5823XHAH/), [IGVFFI8084AYAZ](/sequence-files/IGVFFI8084AYAZ/), [IGVFFI6790GXFV](/sequence-files/IGVFFI6790GXFV/), [IGVFFI0086RCFO](/sequence-files/IGVFFI0086RCFO/), [IGVFFI7583EKHH](/sequence-files/IGVFFI7583EKHH/), [IGVFFI9229HMQG](/sequence-files/IGVFFI9229HMQG/), [IGVFFI6472EHNR](/sequence-files/IGVFFI6472EHNR/) 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/IGVFDS3034JURQ/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM0981PNVB](/in-vitro-systems/IGVFSM0981PNVB/) 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/IGVFSM0981PNVB/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS3034JURQ](/measurement-sets/IGVFDS3034JURQ/) 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/IGVFDS3034JURQ/"
}
]
},
"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": "2023-11-30T22:47:11.320310+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/IGVFFI6538LPYR/",
"accession": "IGVFFI6538LPYR",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinC-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:41:12.520639+00:00",
"file_format": "fastq",
"file_size": 7797948,
"href": "/sequence-files/IGVFFI6538LPYR/@@download/IGVFFI6538LPYR.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/9ef43dea-ac2a-4409-94a4-8d0d54529892/IGVFFI6538LPYR.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-BinC-PCRrep1_S10_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5823XHAH/",
"accession": "IGVFFI5823XHAH",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinC-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:25:48.451192+00:00",
"file_format": "fastq",
"file_size": 3005842,
"href": "/sequence-files/IGVFFI5823XHAH/@@download/IGVFFI5823XHAH.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/c227f1c0-038e-4c9a-aed9-0d5d775c630e/IGVFFI5823XHAH.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-BinC-PCRrep2_S66_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8084AYAZ/",
"accession": "IGVFFI8084AYAZ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinC-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:53:52.512659+00:00",
"file_format": "fastq",
"file_size": 14319962,
"href": "/sequence-files/IGVFFI8084AYAZ/@@download/IGVFFI8084AYAZ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/d936ebe1-46df-42e3-bed0-1d79bd60ab43/IGVFFI8084AYAZ.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-BinC-PCRrep1_S10_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6790GXFV/",
"accession": "IGVFFI6790GXFV",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinC-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:00:28.606913+00:00",
"file_format": "fastq",
"file_size": 13404572,
"href": "/sequence-files/IGVFFI6790GXFV/@@download/IGVFFI6790GXFV.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/9b955282-2f2e-40bd-b3f6-68eae8f84f84/IGVFFI6790GXFV.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-BinC-PCRrep2_S66_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0086RCFO/",
"accession": "IGVFFI0086RCFO",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinC-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:47:30.974877+00:00",
"file_format": "fastq",
"file_size": 7345126,
"href": "/sequence-files/IGVFFI0086RCFO/@@download/IGVFFI0086RCFO.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/c9deaf56-c854-4fb4-b281-99b8bb79aef2/IGVFFI0086RCFO.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-BinC-PCRrep2_S66_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7583EKHH/",
"accession": "IGVFFI7583EKHH",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinC-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:19:27.736340+00:00",
"file_format": "fastq",
"file_size": 3199938,
"href": "/sequence-files/IGVFFI7583EKHH/@@download/IGVFFI7583EKHH.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/a92eb21a-91e3-4f1a-8ed5-07494f1f8b1f/IGVFFI7583EKHH.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-BinC-PCRrep1_S10_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9229HMQG/",
"accession": "IGVFFI9229HMQG",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinC-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:06:58.383978+00:00",
"file_format": "fastq",
"file_size": 3314416,
"href": "/sequence-files/IGVFFI9229HMQG/@@download/IGVFFI9229HMQG.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/f91f70c0-613e-4514-9522-8a8b056c28d9/IGVFFI9229HMQG.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-BinC-PCRrep1_S10_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6472EHNR/",
"accession": "IGVFFI6472EHNR",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinC-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:13:12.285724+00:00",
"file_format": "fastq",
"file_size": 3182976,
"href": "/sequence-files/IGVFFI6472EHNR/@@download/IGVFFI6472EHNR.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/c23df49f-b26f-4940-9508-052e5f45d65d/IGVFFI6472EHNR.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-BinC-PCRrep2_S66_I1_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": "2023-12-20T23:04:56.333367+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0981PNVB/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0981PNVB",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-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": "2023-12-05T18:41:12.520639+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": "bf395a3b-f6b7-439c-a101-bb811ae7ddef"
}