{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1872APYF/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1872APYF",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-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 [IGVFDS1872APYF](/measurement-sets/IGVFDS1872APYF/) has sequence file(s) [IGVFFI8865WRBA](/sequence-files/IGVFFI8865WRBA/), [IGVFFI9302YGJM](/sequence-files/IGVFFI9302YGJM/), [IGVFFI4331GDZK](/sequence-files/IGVFFI4331GDZK/), [IGVFFI5171SVLY](/sequence-files/IGVFFI5171SVLY/), [IGVFFI5669JTGU](/sequence-files/IGVFFI5669JTGU/), [IGVFFI2113HMZS](/sequence-files/IGVFFI2113HMZS/), [IGVFFI9318TVDX](/sequence-files/IGVFFI9318TVDX/), [IGVFFI8763NKPA](/sequence-files/IGVFFI8763NKPA/) 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/IGVFDS1872APYF/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS1872APYF](/measurement-sets/IGVFDS1872APYF/) has sequence file(s): [IGVFFI8865WRBA](/sequence-files/IGVFFI8865WRBA/), [IGVFFI9302YGJM](/sequence-files/IGVFFI9302YGJM/), [IGVFFI4331GDZK](/sequence-files/IGVFFI4331GDZK/), [IGVFFI5171SVLY](/sequence-files/IGVFFI5171SVLY/), [IGVFFI5669JTGU](/sequence-files/IGVFFI5669JTGU/), [IGVFFI2113HMZS](/sequence-files/IGVFFI2113HMZS/), [IGVFFI9318TVDX](/sequence-files/IGVFFI9318TVDX/), [IGVFFI8763NKPA](/sequence-files/IGVFFI8763NKPA/) 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/IGVFDS1872APYF/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM7796ITHX](/in-vitro-systems/IGVFSM7796ITHX/) 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/IGVFSM7796ITHX/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS1872APYF](/measurement-sets/IGVFDS1872APYF/) 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/IGVFDS1872APYF/"
}
]
},
"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": "2023-11-30T22:48:12.818005+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/IGVFFI8865WRBA/",
"accession": "IGVFFI8865WRBA",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinC-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:32:29.105954+00:00",
"file_format": "fastq",
"file_size": 3390018,
"href": "/sequence-files/IGVFFI8865WRBA/@@download/IGVFFI8865WRBA.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/d3ec12a9-cbd6-414b-b82d-204cbd0a9675/IGVFFI8865WRBA.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-BinC-PCRrep2_S193_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9302YGJM/",
"accession": "IGVFFI9302YGJM",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinC-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:24:12.158451+00:00",
"file_format": "fastq",
"file_size": 3323303,
"href": "/sequence-files/IGVFFI9302YGJM/@@download/IGVFFI9302YGJM.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/0b5c604a-5752-483d-bd4d-64deafee8118/IGVFFI9302YGJM.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-BinC-PCRrep2_S193_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4331GDZK/",
"accession": "IGVFFI4331GDZK",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinC-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:59:10.607178+00:00",
"file_format": "fastq",
"file_size": 3323619,
"href": "/sequence-files/IGVFFI4331GDZK/@@download/IGVFFI4331GDZK.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/ad9e5311-cbf0-4f2b-a73f-a4522b728a24/IGVFFI4331GDZK.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-BinC-PCRrep1_S136_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5171SVLY/",
"accession": "IGVFFI5171SVLY",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinC-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:07:23.284757+00:00",
"file_format": "fastq",
"file_size": 8058058,
"href": "/sequence-files/IGVFFI5171SVLY/@@download/IGVFFI5171SVLY.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/3c171ec1-6a16-44c8-81bb-e17270ce3b3e/IGVFFI5171SVLY.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-BinC-PCRrep2_S193_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5669JTGU/",
"accession": "IGVFFI5669JTGU",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinC-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:51:03.467653+00:00",
"file_format": "fastq",
"file_size": 3389462,
"href": "/sequence-files/IGVFFI5669JTGU/@@download/IGVFFI5669JTGU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/f1c180af-caa0-4347-8c03-5c85956993ca/IGVFFI5669JTGU.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-BinC-PCRrep1_S136_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2113HMZS/",
"accession": "IGVFFI2113HMZS",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinC-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:42:35.061474+00:00",
"file_format": "fastq",
"file_size": 14677365,
"href": "/sequence-files/IGVFFI2113HMZS/@@download/IGVFFI2113HMZS.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/f8ba5dd8-1314-4e52-a0b6-e3819ba6bb25/IGVFFI2113HMZS.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-BinC-PCRrep1_S136_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9318TVDX/",
"accession": "IGVFFI9318TVDX",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinC-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:34:11.651201+00:00",
"file_format": "fastq",
"file_size": 7988472,
"href": "/sequence-files/IGVFFI9318TVDX/@@download/IGVFFI9318TVDX.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/f054d44d-6ebf-4d1a-9f5c-ab7ceff7448e/IGVFFI9318TVDX.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-BinC-PCRrep1_S136_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8763NKPA/",
"accession": "IGVFFI8763NKPA",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinC-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:15:46.059624+00:00",
"file_format": "fastq",
"file_size": 14970079,
"href": "/sequence-files/IGVFFI8763NKPA/@@download/IGVFFI8763NKPA.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/85c9b365-1667-413f-ad49-fc8f2be6eaa3/IGVFFI8763NKPA.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-BinC-PCRrep2_S193_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": "2023-12-20T23:04:13.290371+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7796ITHX/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7796ITHX",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-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) 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": "2023-12-05T19:34:11.651201+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": "81692274-2e76-47bb-bcae-0b4e940e2abf"
}