{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4551ZTES/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4551ZTES",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinA_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 [IGVFSM2813ICIH](/in-vitro-systems/IGVFSM2813ICIH/) 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/IGVFSM2813ICIH/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS4551ZTES](/measurement-sets/IGVFDS4551ZTES/) has sequence file(s) [IGVFFI3211CLSS](/sequence-files/IGVFFI3211CLSS/), [IGVFFI7195YCTG](/sequence-files/IGVFFI7195YCTG/), [IGVFFI5397YNGR](/sequence-files/IGVFFI5397YNGR/), [IGVFFI5817JJDY](/sequence-files/IGVFFI5817JJDY/), [IGVFFI5419MLDE](/sequence-files/IGVFFI5419MLDE/), [IGVFFI3853IUHT](/sequence-files/IGVFFI3853IUHT/), [IGVFFI2727RDWL](/sequence-files/IGVFFI2727RDWL/), [IGVFFI2361BJJJ](/sequence-files/IGVFFI2361BJJJ/) 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/IGVFDS4551ZTES/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS4551ZTES](/measurement-sets/IGVFDS4551ZTES/) has sequence file(s): [IGVFFI3211CLSS](/sequence-files/IGVFFI3211CLSS/), [IGVFFI7195YCTG](/sequence-files/IGVFFI7195YCTG/), [IGVFFI5397YNGR](/sequence-files/IGVFFI5397YNGR/), [IGVFFI5817JJDY](/sequence-files/IGVFFI5817JJDY/), [IGVFFI5419MLDE](/sequence-files/IGVFFI5419MLDE/), [IGVFFI3853IUHT](/sequence-files/IGVFFI3853IUHT/), [IGVFFI2727RDWL](/sequence-files/IGVFFI2727RDWL/), [IGVFFI2361BJJJ](/sequence-files/IGVFFI2361BJJJ/) 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/IGVFDS4551ZTES/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS4551ZTES](/measurement-sets/IGVFDS4551ZTES/) 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/IGVFDS4551ZTES/"
}
]
},
"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": "2023-12-01T00:02:51.408453+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/IGVFFI3211CLSS/",
"accession": "IGVFFI3211CLSS",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinA-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:59:03.042976+00:00",
"file_format": "fastq",
"file_size": 14175642,
"href": "/sequence-files/IGVFFI3211CLSS/@@download/IGVFFI3211CLSS.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/ed4536c7-6a5e-4958-a01f-78fccdaf06ea/IGVFFI3211CLSS.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_S2-BioRep1-FFRep1-BinA-PCRrep2_S57_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7195YCTG/",
"accession": "IGVFFI7195YCTG",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinA-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:24:29.113811+00:00",
"file_format": "fastq",
"file_size": 3158732,
"href": "/sequence-files/IGVFFI7195YCTG/@@download/IGVFFI7195YCTG.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/cfacee96-f6f6-4e43-ab38-bbfbd6b08e98/IGVFFI7195YCTG.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_S2-BioRep1-FFRep1-BinA-PCRrep2_S57_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5397YNGR/",
"accession": "IGVFFI5397YNGR",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinA-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:05:40.222940+00:00",
"file_format": "fastq",
"file_size": 3251472,
"href": "/sequence-files/IGVFFI5397YNGR/@@download/IGVFFI5397YNGR.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/72c1f5d0-caff-4fa5-941d-3f88fae19338/IGVFFI5397YNGR.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_S2-BioRep1-FFRep1-BinA-PCRrep1_S1_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5817JJDY/",
"accession": "IGVFFI5817JJDY",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinA-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:52:30.345355+00:00",
"file_format": "fastq",
"file_size": 14517553,
"href": "/sequence-files/IGVFFI5817JJDY/@@download/IGVFFI5817JJDY.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/a227c7b3-e184-421b-b4ae-93ff1732fa52/IGVFFI5817JJDY.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_S2-BioRep1-FFRep1-BinA-PCRrep1_S1_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5419MLDE/",
"accession": "IGVFFI5419MLDE",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinA-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:11:53.451448+00:00",
"file_format": "fastq",
"file_size": 3202885,
"href": "/sequence-files/IGVFFI5419MLDE/@@download/IGVFFI5419MLDE.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/0264836d-9210-4d83-a863-259ad381eee6/IGVFFI5419MLDE.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_S2-BioRep1-FFRep1-BinA-PCRrep2_S57_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3853IUHT/",
"accession": "IGVFFI3853IUHT",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinA-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:18:08.642129+00:00",
"file_format": "fastq",
"file_size": 3220069,
"href": "/sequence-files/IGVFFI3853IUHT/@@download/IGVFFI3853IUHT.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/f1855f1c-81b9-4164-8fec-319a3cf2e2fa/IGVFFI3853IUHT.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_S2-BioRep1-FFRep1-BinA-PCRrep1_S1_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2727RDWL/",
"accession": "IGVFFI2727RDWL",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinA-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:39:48.156862+00:00",
"file_format": "fastq",
"file_size": 7937867,
"href": "/sequence-files/IGVFFI2727RDWL/@@download/IGVFFI2727RDWL.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/e45c57e4-67a7-4127-8d48-2416f6765645/IGVFFI2727RDWL.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_S2-BioRep1-FFRep1-BinA-PCRrep1_S1_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2361BJJJ/",
"accession": "IGVFFI2361BJJJ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinA-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:46:11.481533+00:00",
"file_format": "fastq",
"file_size": 7764855,
"href": "/sequence-files/IGVFFI2361BJJJ/@@download/IGVFFI2361BJJJ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/aef797eb-f060-4b09-b860-7c51f325c601/IGVFFI2361BJJJ.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_S2-BioRep1-FFRep1-BinA-PCRrep2_S57_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": "2023-12-20T23:10:19.286826+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2813ICIH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2813ICIH",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinA"
],
"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 0-10% 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": "2023-12-05T18:39:48.156862+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": "ecd95d59-d523-4401-8ab0-ec245f82498d"
}