{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3789TNPM/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3789TNPM",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep1-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 [IGVFDS3789TNPM](/measurement-sets/IGVFDS3789TNPM/) has sequence file(s) [IGVFFI3887WMEP](/sequence-files/IGVFFI3887WMEP/), [IGVFFI7297UNKC](/sequence-files/IGVFFI7297UNKC/), [IGVFFI0142JETR](/sequence-files/IGVFFI0142JETR/), [IGVFFI3092NYHM](/sequence-files/IGVFFI3092NYHM/), [IGVFFI0107RZJE](/sequence-files/IGVFFI0107RZJE/), [IGVFFI9951PHCD](/sequence-files/IGVFFI9951PHCD/), [IGVFFI4661TOQV](/sequence-files/IGVFFI4661TOQV/), [IGVFFI3108IPZM](/sequence-files/IGVFFI3108IPZM/) 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/IGVFDS3789TNPM/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS3789TNPM](/measurement-sets/IGVFDS3789TNPM/) has sequence file(s): [IGVFFI3887WMEP](/sequence-files/IGVFFI3887WMEP/), [IGVFFI7297UNKC](/sequence-files/IGVFFI7297UNKC/), [IGVFFI0142JETR](/sequence-files/IGVFFI0142JETR/), [IGVFFI3092NYHM](/sequence-files/IGVFFI3092NYHM/), [IGVFFI0107RZJE](/sequence-files/IGVFFI0107RZJE/), [IGVFFI9951PHCD](/sequence-files/IGVFFI9951PHCD/), [IGVFFI4661TOQV](/sequence-files/IGVFFI4661TOQV/), [IGVFFI3108IPZM](/sequence-files/IGVFFI3108IPZM/) 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/IGVFDS3789TNPM/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM6662LPXP](/in-vitro-systems/IGVFSM6662LPXP/) 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/IGVFSM6662LPXP/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS3789TNPM](/measurement-sets/IGVFDS3789TNPM/) 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/IGVFDS3789TNPM/"
}
]
},
"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": "2023-11-30T22:47:48.300125+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/IGVFFI3887WMEP/",
"accession": "IGVFFI3887WMEP",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinC-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:29:21.883389+00:00",
"file_format": "fastq",
"file_size": 3093065,
"href": "/sequence-files/IGVFFI3887WMEP/@@download/IGVFFI3887WMEP.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/a96be181-1983-4161-93c1-ddb37b66957f/IGVFFI3887WMEP.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_S12-BioRep1-FFRep1-BinC-PCRrep2_S172_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7297UNKC/",
"accession": "IGVFFI7297UNKC",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinC-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:31:02.077597+00:00",
"file_format": "fastq",
"file_size": 7480972,
"href": "/sequence-files/IGVFFI7297UNKC/@@download/IGVFFI7297UNKC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/675605f7-dfaa-4fbe-b394-ac6996d0d4f1/IGVFFI7297UNKC.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_S12-BioRep1-FFRep1-BinC-PCRrep1_S115_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0142JETR/",
"accession": "IGVFFI0142JETR",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinC-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:47:55.850009+00:00",
"file_format": "fastq",
"file_size": 3225487,
"href": "/sequence-files/IGVFFI0142JETR/@@download/IGVFFI0142JETR.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/001b617a-d82d-49b8-9e5f-9f4730e5b2da/IGVFFI0142JETR.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_S12-BioRep1-FFRep1-BinC-PCRrep1_S115_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3092NYHM/",
"accession": "IGVFFI3092NYHM",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinC-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:04:15.611519+00:00",
"file_format": "fastq",
"file_size": 7441842,
"href": "/sequence-files/IGVFFI3092NYHM/@@download/IGVFFI3092NYHM.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/1256e920-b78e-44ed-817a-1958137a94d7/IGVFFI3092NYHM.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_S12-BioRep1-FFRep1-BinC-PCRrep2_S172_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0107RZJE/",
"accession": "IGVFFI0107RZJE",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinC-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:21:05.392730+00:00",
"file_format": "fastq",
"file_size": 3177229,
"href": "/sequence-files/IGVFFI0107RZJE/@@download/IGVFFI0107RZJE.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/ab29af81-79fb-4c87-9b37-91a4ef81e4a2/IGVFFI0107RZJE.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_S12-BioRep1-FFRep1-BinC-PCRrep2_S172_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9951PHCD/",
"accession": "IGVFFI9951PHCD",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinC-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:56:08.289487+00:00",
"file_format": "fastq",
"file_size": 3118230,
"href": "/sequence-files/IGVFFI9951PHCD/@@download/IGVFFI9951PHCD.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/b8ab28ef-f887-4ba1-8fa2-53b5828a4edc/IGVFFI9951PHCD.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_S12-BioRep1-FFRep1-BinC-PCRrep1_S115_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4661TOQV/",
"accession": "IGVFFI4661TOQV",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinC-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:39:22.621872+00:00",
"file_format": "fastq",
"file_size": 13825074,
"href": "/sequence-files/IGVFFI4661TOQV/@@download/IGVFFI4661TOQV.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/c18bd7ee-e8aa-4109-bd9b-95b3f4720123/IGVFFI4661TOQV.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_S12-BioRep1-FFRep1-BinC-PCRrep1_S115_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3108IPZM/",
"accession": "IGVFFI3108IPZM",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinC-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:12:33.883348+00:00",
"file_format": "fastq",
"file_size": 13708868,
"href": "/sequence-files/IGVFFI3108IPZM/@@download/IGVFFI3108IPZM.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/82568a63-b9ee-4e49-a2ac-bfa05ca9ebd8/IGVFFI3108IPZM.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_S12-BioRep1-FFRep1-BinC-PCRrep2_S172_R2_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": "2023-12-20T23:10:54.565071+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM6662LPXP/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6662LPXP",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep1-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) 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": "2023-12-05T19:31:02.077597+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": "2ec7a716-f8ac-4338-b11b-eb88667e3ac7"
}