{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6332JYBE/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6332JYBE",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinB_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 [IGVFSM2342HMUU](/in-vitro-systems/IGVFSM2342HMUU/) 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/IGVFSM2342HMUU/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS6332JYBE](/measurement-sets/IGVFDS6332JYBE/) has sequence file(s) [IGVFFI9524NRQF](/sequence-files/IGVFFI9524NRQF/), [IGVFFI7592SAVE](/sequence-files/IGVFFI7592SAVE/), [IGVFFI4805KFCV](/sequence-files/IGVFFI4805KFCV/), [IGVFFI6682IYBP](/sequence-files/IGVFFI6682IYBP/), [IGVFFI6326ZIXH](/sequence-files/IGVFFI6326ZIXH/), [IGVFFI7611OVVQ](/sequence-files/IGVFFI7611OVVQ/), [IGVFFI6879WFZJ](/sequence-files/IGVFFI6879WFZJ/), [IGVFFI9061DTGP](/sequence-files/IGVFFI9061DTGP/) 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/IGVFDS6332JYBE/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS6332JYBE](/measurement-sets/IGVFDS6332JYBE/) has sequence file(s): [IGVFFI9524NRQF](/sequence-files/IGVFFI9524NRQF/), [IGVFFI7592SAVE](/sequence-files/IGVFFI7592SAVE/), [IGVFFI4805KFCV](/sequence-files/IGVFFI4805KFCV/), [IGVFFI6682IYBP](/sequence-files/IGVFFI6682IYBP/), [IGVFFI6326ZIXH](/sequence-files/IGVFFI6326ZIXH/), [IGVFFI7611OVVQ](/sequence-files/IGVFFI7611OVVQ/), [IGVFFI6879WFZJ](/sequence-files/IGVFFI6879WFZJ/), [IGVFFI9061DTGP](/sequence-files/IGVFFI9061DTGP/) 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/IGVFDS6332JYBE/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS6332JYBE](/measurement-sets/IGVFDS6332JYBE/) 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/IGVFDS6332JYBE/"
}
]
},
"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": "2023-11-30T22:48:11.871152+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/IGVFFI9524NRQF/",
"accession": "IGVFFI9524NRQF",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinB-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:50:54.643448+00:00",
"file_format": "fastq",
"file_size": 3345516,
"href": "/sequence-files/IGVFFI9524NRQF/@@download/IGVFFI9524NRQF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/65c52257-f3e7-40e9-84ca-bce1a5b7af2f/IGVFFI9524NRQF.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-BinB-PCRrep1_S135_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7592SAVE/",
"accession": "IGVFFI7592SAVE",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinB-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:07:14.495367+00:00",
"file_format": "fastq",
"file_size": 8017281,
"href": "/sequence-files/IGVFFI7592SAVE/@@download/IGVFFI7592SAVE.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/53c93318-7d13-4917-83a4-3ba15da6bca3/IGVFFI7592SAVE.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-BinB-PCRrep2_S192_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4805KFCV/",
"accession": "IGVFFI4805KFCV",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinB-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:32:20.247014+00:00",
"file_format": "fastq",
"file_size": 3335059,
"href": "/sequence-files/IGVFFI4805KFCV/@@download/IGVFFI4805KFCV.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/e77f9463-4b44-41c8-aa9b-f4160963bee1/IGVFFI4805KFCV.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-BinB-PCRrep2_S192_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6682IYBP/",
"accession": "IGVFFI6682IYBP",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinB-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:15:36.840111+00:00",
"file_format": "fastq",
"file_size": 14763190,
"href": "/sequence-files/IGVFFI6682IYBP/@@download/IGVFFI6682IYBP.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/4cf2f24b-7f0f-4f2c-a463-48ac4661345b/IGVFFI6682IYBP.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-BinB-PCRrep2_S192_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6326ZIXH/",
"accession": "IGVFFI6326ZIXH",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinB-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:59:01.883425+00:00",
"file_format": "fastq",
"file_size": 3215634,
"href": "/sequence-files/IGVFFI6326ZIXH/@@download/IGVFFI6326ZIXH.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/4b0aaaff-ff94-4c01-aebc-6d1df52aff26/IGVFFI6326ZIXH.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-BinB-PCRrep1_S135_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7611OVVQ/",
"accession": "IGVFFI7611OVVQ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinB-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:24:03.433499+00:00",
"file_format": "fastq",
"file_size": 3270556,
"href": "/sequence-files/IGVFFI7611OVVQ/@@download/IGVFFI7611OVVQ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/6560705c-7bc4-44e1-8722-51b349783e12/IGVFFI7611OVVQ.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-BinB-PCRrep2_S192_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6879WFZJ/",
"accession": "IGVFFI6879WFZJ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinB-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:34:02.753046+00:00",
"file_format": "fastq",
"file_size": 7710770,
"href": "/sequence-files/IGVFFI6879WFZJ/@@download/IGVFFI6879WFZJ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/a0e3f2fd-c769-41f8-b1ff-95ec449b10c7/IGVFFI6879WFZJ.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S16-BioRep2-FFRep2-BinB-PCRrep1_S135_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9061DTGP/",
"accession": "IGVFFI9061DTGP",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinB-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:42:25.942572+00:00",
"file_format": "fastq",
"file_size": 14248386,
"href": "/sequence-files/IGVFFI9061DTGP/@@download/IGVFFI9061DTGP.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/462df46e-9915-4bc9-897a-fe34671adf97/IGVFFI9061DTGP.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S16-BioRep2-FFRep2-BinB-PCRrep1_S135_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": "2023-12-20T23:11:18.908932+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2342HMUU/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2342HMUU",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinB"
],
"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 11-20% 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": "2023-12-05T19:34:02.753046+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": "a5090fb9-a707-4d92-b09d-f65f88462143"
}