{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1861LEUZ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1861LEUZ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-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": "mismatched status",
"detail": "Released in vitro system [IGVFSM9814YUSQ](/in-vitro-systems/IGVFSM9814YUSQ/) 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/IGVFSM9814YUSQ/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS1861LEUZ](/measurement-sets/IGVFDS1861LEUZ/) has sequence file(s) [IGVFFI1148OPQE](/sequence-files/IGVFFI1148OPQE/), [IGVFFI5963LEBX](/sequence-files/IGVFFI5963LEBX/), [IGVFFI0385ZFTM](/sequence-files/IGVFFI0385ZFTM/), [IGVFFI9396ZTXP](/sequence-files/IGVFFI9396ZTXP/), [IGVFFI9546INOY](/sequence-files/IGVFFI9546INOY/), [IGVFFI7461LOTH](/sequence-files/IGVFFI7461LOTH/), [IGVFFI6740UOLT](/sequence-files/IGVFFI6740UOLT/), [IGVFFI6597VGAG](/sequence-files/IGVFFI6597VGAG/) 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/IGVFDS1861LEUZ/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS1861LEUZ](/measurement-sets/IGVFDS1861LEUZ/) has sequence file(s): [IGVFFI1148OPQE](/sequence-files/IGVFFI1148OPQE/), [IGVFFI5963LEBX](/sequence-files/IGVFFI5963LEBX/), [IGVFFI0385ZFTM](/sequence-files/IGVFFI0385ZFTM/), [IGVFFI9396ZTXP](/sequence-files/IGVFFI9396ZTXP/), [IGVFFI9546INOY](/sequence-files/IGVFFI9546INOY/), [IGVFFI7461LOTH](/sequence-files/IGVFFI7461LOTH/), [IGVFFI6740UOLT](/sequence-files/IGVFFI6740UOLT/), [IGVFFI6597VGAG](/sequence-files/IGVFFI6597VGAG/) 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/IGVFDS1861LEUZ/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS1861LEUZ](/measurement-sets/IGVFDS1861LEUZ/) 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/IGVFDS1861LEUZ/"
}
]
},
"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": "2023-11-30T22:48:35.593116+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/IGVFFI1148OPQE/",
"accession": "IGVFFI1148OPQE",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep1-BinC-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:54:06.346229+00:00",
"file_format": "fastq",
"file_size": 3159816,
"href": "/sequence-files/IGVFFI1148OPQE/@@download/IGVFFI1148OPQE.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/bd2e0df0-55b2-49f7-b857-0fa7c5ea4d58/IGVFFI1148OPQE.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_S19-BioRep4-FFRep1-BinC-PCRrep1_S157_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5963LEBX/",
"accession": "IGVFFI5963LEBX",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep1-BinC-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:27:19.736277+00:00",
"file_format": "fastq",
"file_size": 3022391,
"href": "/sequence-files/IGVFFI5963LEBX/@@download/IGVFFI5963LEBX.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/87d916f8-92b3-49ca-bac4-2066671f9c01/IGVFFI5963LEBX.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_S19-BioRep4-FFRep1-BinC-PCRrep2_S214_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0385ZFTM/",
"accession": "IGVFFI0385ZFTM",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep1-BinC-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:02:13.837460+00:00",
"file_format": "fastq",
"file_size": 3147184,
"href": "/sequence-files/IGVFFI0385ZFTM/@@download/IGVFFI0385ZFTM.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/9f797e17-1b85-486a-8619-03337ae2e0fb/IGVFFI0385ZFTM.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_S19-BioRep4-FFRep1-BinC-PCRrep1_S157_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9396ZTXP/",
"accession": "IGVFFI9396ZTXP",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep1-BinC-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:35:32.892392+00:00",
"file_format": "fastq",
"file_size": 3026558,
"href": "/sequence-files/IGVFFI9396ZTXP/@@download/IGVFFI9396ZTXP.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/b4253387-1851-4da9-ab92-3008aa93b8a3/IGVFFI9396ZTXP.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_S19-BioRep4-FFRep1-BinC-PCRrep2_S214_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9546INOY/",
"accession": "IGVFFI9546INOY",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep1-BinC-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:37:17.398065+00:00",
"file_format": "fastq",
"file_size": 7529163,
"href": "/sequence-files/IGVFFI9546INOY/@@download/IGVFFI9546INOY.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/c2372aec-1e00-43ca-b25d-83ee97956ef2/IGVFFI9546INOY.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_S19-BioRep4-FFRep1-BinC-PCRrep1_S157_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7461LOTH/",
"accession": "IGVFFI7461LOTH",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep1-BinC-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:18:58.160204+00:00",
"file_format": "fastq",
"file_size": 13429015,
"href": "/sequence-files/IGVFFI7461LOTH/@@download/IGVFFI7461LOTH.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/918cd0dc-7f1b-410f-909f-9df767d3513e/IGVFFI7461LOTH.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_S19-BioRep4-FFRep1-BinC-PCRrep2_S214_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6740UOLT/",
"accession": "IGVFFI6740UOLT",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep1-BinC-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:10:29.249710+00:00",
"file_format": "fastq",
"file_size": 7219406,
"href": "/sequence-files/IGVFFI6740UOLT/@@download/IGVFFI6740UOLT.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/0245b5d2-8790-46f7-ab96-0cef842987b3/IGVFFI6740UOLT.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_S19-BioRep4-FFRep1-BinC-PCRrep2_S214_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6597VGAG/",
"accession": "IGVFFI6597VGAG",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep1-BinC-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:45:47.529684+00:00",
"file_format": "fastq",
"file_size": 13845104,
"href": "/sequence-files/IGVFFI6597VGAG/@@download/IGVFFI6597VGAG.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/ac7be024-f98f-4a2e-9abc-14e7baf2a0f9/IGVFFI6597VGAG.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_S19-BioRep4-FFRep1-BinC-PCRrep1_S157_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": "2023-12-20T23:10:16.765489+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9814YUSQ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9814YUSQ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-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": "2023-12-05T19:37:17.398065+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": "55b6e5e2-92d9-4f79-b5f7-d296f7d52d58"
}