{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1097QQST/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1097QQST",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinF_AmpliconSequencing"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"status": "released",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM7762ZCFL](/in-vitro-systems/IGVFSM7762ZCFL/) 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/IGVFSM7762ZCFL/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS1097QQST](/measurement-sets/IGVFDS1097QQST/) has sequence file(s) [IGVFFI5682TOJO](/sequence-files/IGVFFI5682TOJO/), [IGVFFI0975HKEC](/sequence-files/IGVFFI0975HKEC/), [IGVFFI8443LNVL](/sequence-files/IGVFFI8443LNVL/), [IGVFFI3729TEUC](/sequence-files/IGVFFI3729TEUC/), [IGVFFI7099LDFV](/sequence-files/IGVFFI7099LDFV/), [IGVFFI0045RSIV](/sequence-files/IGVFFI0045RSIV/), [IGVFFI1846HTDE](/sequence-files/IGVFFI1846HTDE/), [IGVFFI0206REMJ](/sequence-files/IGVFFI0206REMJ/) 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/IGVFDS1097QQST/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS1097QQST](/measurement-sets/IGVFDS1097QQST/) has sequence file(s): [IGVFFI5682TOJO](/sequence-files/IGVFFI5682TOJO/), [IGVFFI0975HKEC](/sequence-files/IGVFFI0975HKEC/), [IGVFFI8443LNVL](/sequence-files/IGVFFI8443LNVL/), [IGVFFI3729TEUC](/sequence-files/IGVFFI3729TEUC/), [IGVFFI7099LDFV](/sequence-files/IGVFFI7099LDFV/), [IGVFFI0045RSIV](/sequence-files/IGVFFI0045RSIV/), [IGVFFI1846HTDE](/sequence-files/IGVFFI1846HTDE/), [IGVFFI0206REMJ](/sequence-files/IGVFFI0206REMJ/) 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/IGVFDS1097QQST/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS1097QQST](/measurement-sets/IGVFDS1097QQST/) 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/IGVFDS1097QQST/"
}
]
},
"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": "2023-11-30T22:48:16.050174+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/IGVFFI5682TOJO/",
"accession": "IGVFFI5682TOJO",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinF-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:59:36.694316+00:00",
"file_format": "fastq",
"file_size": 3143048,
"href": "/sequence-files/IGVFFI5682TOJO/@@download/IGVFFI5682TOJO.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/572f1ce6-ab42-485a-8ba9-0d6da2c12a2e/IGVFFI5682TOJO.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_pPPIF2_S16-BioRep2-FFRep2-BinF-PCRrep1_S139_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0975HKEC/",
"accession": "IGVFFI0975HKEC",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinF-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:43:02.463549+00:00",
"file_format": "fastq",
"file_size": 14015380,
"href": "/sequence-files/IGVFFI0975HKEC/@@download/IGVFFI0975HKEC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/1aa7cba5-acbe-45aa-b003-56df82bbac15/IGVFFI0975HKEC.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_pPPIF2_S16-BioRep2-FFRep2-BinF-PCRrep1_S139_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8443LNVL/",
"accession": "IGVFFI8443LNVL",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinF-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:51:29.623502+00:00",
"file_format": "fastq",
"file_size": 3176332,
"href": "/sequence-files/IGVFFI8443LNVL/@@download/IGVFFI8443LNVL.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/a7c84d67-bb3d-4977-b21b-73a58d376acc/IGVFFI8443LNVL.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_pPPIF2_S16-BioRep2-FFRep2-BinF-PCRrep1_S139_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3729TEUC/",
"accession": "IGVFFI3729TEUC",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinF-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:32:55.138003+00:00",
"file_format": "fastq",
"file_size": 3349644,
"href": "/sequence-files/IGVFFI3729TEUC/@@download/IGVFFI3729TEUC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/5fc5fe0e-1cd1-42d2-a0a1-6377327d9fb0/IGVFFI3729TEUC.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_pPPIF2_S16-BioRep2-FFRep2-BinF-PCRrep2_S196_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7099LDFV/",
"accession": "IGVFFI7099LDFV",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinF-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:24:42.154455+00:00",
"file_format": "fastq",
"file_size": 3688399,
"href": "/sequence-files/IGVFFI7099LDFV/@@download/IGVFFI7099LDFV.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/f03b32b9-1e5d-49ad-9853-589555d98ac8/IGVFFI7099LDFV.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_pPPIF2_S16-BioRep2-FFRep2-BinF-PCRrep2_S196_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0045RSIV/",
"accession": "IGVFFI0045RSIV",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinF-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:07:49.506365+00:00",
"file_format": "fastq",
"file_size": 7975455,
"href": "/sequence-files/IGVFFI0045RSIV/@@download/IGVFFI0045RSIV.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/bb610938-9948-4ce4-bc25-9ffa15f4b56f/IGVFFI0045RSIV.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_pPPIF2_S16-BioRep2-FFRep2-BinF-PCRrep2_S196_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1846HTDE/",
"accession": "IGVFFI1846HTDE",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinF-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:16:14.037800+00:00",
"file_format": "fastq",
"file_size": 14815924,
"href": "/sequence-files/IGVFFI1846HTDE/@@download/IGVFFI1846HTDE.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/b47fcb0b-96f4-4ee2-bc5d-e0cef4d3f69d/IGVFFI1846HTDE.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_pPPIF2_S16-BioRep2-FFRep2-BinF-PCRrep2_S196_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0206REMJ/",
"accession": "IGVFFI0206REMJ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinF-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:34:38.243432+00:00",
"file_format": "fastq",
"file_size": 7480935,
"href": "/sequence-files/IGVFFI0206REMJ/@@download/IGVFFI0206REMJ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/ea5b3aac-0e34-4e87-a11e-ae75f08eb71a/IGVFFI0206REMJ.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_pPPIF2_S16-BioRep2-FFRep2-BinF-PCRrep1_S139_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS1863TJOE/"
],
"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": "2023-12-20T23:05:02.868669+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7762ZCFL/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7762ZCFL",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep2-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) treated with 100 ng/mL phorbol 13-acetate 12-myristate for 4 hours, 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 4 hours, modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transfected with a guide library",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/df02c0d4-f796-4f77-bfbc-388cdbfcc615/",
"status": "released",
"treatment_term_name": "T-cell surface glycoprotein CD3 gamma chain"
},
{
"@id": "/treatments/42b3c61d-38de-4bd2-bb39-33c125a417cb/",
"status": "released",
"treatment_term_name": "phorbol 13-acetate 12-myristate"
}
]
}
],
"schema_version": "23",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T19:34:38.243432+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": "d301c825-07a0-4bb6-83cc-06af99b39e7f"
}