{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3736NHYM/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3736NHYM",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinE_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 [IGVFDS3736NHYM](/measurement-sets/IGVFDS3736NHYM/) has sequence file(s) [IGVFFI6449XFPQ](/sequence-files/IGVFFI6449XFPQ/), [IGVFFI0762HJGW](/sequence-files/IGVFFI0762HJGW/), [IGVFFI3187ADME](/sequence-files/IGVFFI3187ADME/), [IGVFFI8817UIFX](/sequence-files/IGVFFI8817UIFX/), [IGVFFI2863IRCD](/sequence-files/IGVFFI2863IRCD/), [IGVFFI2372UIQN](/sequence-files/IGVFFI2372UIQN/), [IGVFFI5139GLYR](/sequence-files/IGVFFI5139GLYR/), [IGVFFI5163QKHM](/sequence-files/IGVFFI5163QKHM/) 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/IGVFDS3736NHYM/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS3736NHYM](/measurement-sets/IGVFDS3736NHYM/) has sequence file(s): [IGVFFI6449XFPQ](/sequence-files/IGVFFI6449XFPQ/), [IGVFFI0762HJGW](/sequence-files/IGVFFI0762HJGW/), [IGVFFI3187ADME](/sequence-files/IGVFFI3187ADME/), [IGVFFI8817UIFX](/sequence-files/IGVFFI8817UIFX/), [IGVFFI2863IRCD](/sequence-files/IGVFFI2863IRCD/), [IGVFFI2372UIQN](/sequence-files/IGVFFI2372UIQN/), [IGVFFI5139GLYR](/sequence-files/IGVFFI5139GLYR/), [IGVFFI5163QKHM](/sequence-files/IGVFFI5163QKHM/) 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/IGVFDS3736NHYM/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM1661ZFEH](/in-vitro-systems/IGVFSM1661ZFEH/) 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/IGVFSM1661ZFEH/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS3736NHYM](/measurement-sets/IGVFDS3736NHYM/) 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/IGVFDS3736NHYM/"
}
]
},
"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": "2023-11-30T22:47:20.230536+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/IGVFFI6449XFPQ/",
"accession": "IGVFFI6449XFPQ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinE-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:27:05.926031+00:00",
"file_format": "fastq",
"file_size": 3217064,
"href": "/sequence-files/IGVFFI6449XFPQ/@@download/IGVFFI6449XFPQ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/f27791df-0949-4708-951c-5a4824c53264/IGVFFI6449XFPQ.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_S5-BioRep2-FFRep1-BinE-PCRrep2_S75_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0762HJGW/",
"accession": "IGVFFI0762HJGW",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinE-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:55:14.365945+00:00",
"file_format": "fastq",
"file_size": 13386422,
"href": "/sequence-files/IGVFFI0762HJGW/@@download/IGVFFI0762HJGW.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/394734ab-1bc4-4f6b-8925-bd1cd27773ef/IGVFFI0762HJGW.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_S5-BioRep2-FFRep1-BinE-PCRrep1_S19_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3187ADME/",
"accession": "IGVFFI3187ADME",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinE-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:42:31.785595+00:00",
"file_format": "fastq",
"file_size": 7312236,
"href": "/sequence-files/IGVFFI3187ADME/@@download/IGVFFI3187ADME.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/92ac6729-deec-41cb-9110-9d0c3eac8d4d/IGVFFI3187ADME.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_S5-BioRep2-FFRep1-BinE-PCRrep1_S19_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8817UIFX/",
"accession": "IGVFFI8817UIFX",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinE-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:01:52.075704+00:00",
"file_format": "fastq",
"file_size": 14344286,
"href": "/sequence-files/IGVFFI8817UIFX/@@download/IGVFFI8817UIFX.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/86735357-25f4-4560-a93f-e0c50b77a9f5/IGVFFI8817UIFX.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_S5-BioRep2-FFRep1-BinE-PCRrep2_S75_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2863IRCD/",
"accession": "IGVFFI2863IRCD",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinE-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:20:45.860134+00:00",
"file_format": "fastq",
"file_size": 3005472,
"href": "/sequence-files/IGVFFI2863IRCD/@@download/IGVFFI2863IRCD.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/b0a17746-64de-40f5-ade4-76a3c98fa380/IGVFFI2863IRCD.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_S5-BioRep2-FFRep1-BinE-PCRrep1_S19_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2372UIQN/",
"accession": "IGVFFI2372UIQN",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinE-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:08:15.136632+00:00",
"file_format": "fastq",
"file_size": 3141860,
"href": "/sequence-files/IGVFFI2372UIQN/@@download/IGVFFI2372UIQN.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/1269bf75-b61f-4910-b9a5-77db960b3687/IGVFFI2372UIQN.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_S5-BioRep2-FFRep1-BinE-PCRrep1_S19_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5139GLYR/",
"accession": "IGVFFI5139GLYR",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinE-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:14:30.540982+00:00",
"file_format": "fastq",
"file_size": 3274434,
"href": "/sequence-files/IGVFFI5139GLYR/@@download/IGVFFI5139GLYR.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/d809a1d6-b800-4d82-96cb-2b7b1510c384/IGVFFI5139GLYR.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_S5-BioRep2-FFRep1-BinE-PCRrep2_S75_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5163QKHM/",
"accession": "IGVFFI5163QKHM",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinE-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:48:50.115627+00:00",
"file_format": "fastq",
"file_size": 7842857,
"href": "/sequence-files/IGVFFI5163QKHM/@@download/IGVFFI5163QKHM.fastq.gz",
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"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_S5-BioRep2-FFRep1-BinE-PCRrep2_S75_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": "2023-12-20T23:04:17.993983+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1661ZFEH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1661ZFEH",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinE"
],
"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 80-90% 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": "2023-12-05T18:42:31.785595+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": "4c8b4ca1-473f-40db-aaf6-0c9b9137f6f3"
}