{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7378VQMR/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7378VQMR",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinF_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 [IGVFDS7378VQMR](/measurement-sets/IGVFDS7378VQMR/) has sequence file(s) [IGVFFI1833ZNCI](/sequence-files/IGVFFI1833ZNCI/), [IGVFFI5528AVXR](/sequence-files/IGVFFI5528AVXR/), [IGVFFI2338CLUZ](/sequence-files/IGVFFI2338CLUZ/), [IGVFFI1777GIOF](/sequence-files/IGVFFI1777GIOF/), [IGVFFI3872OVQC](/sequence-files/IGVFFI3872OVQC/), [IGVFFI2043WQOK](/sequence-files/IGVFFI2043WQOK/), [IGVFFI0826BDAP](/sequence-files/IGVFFI0826BDAP/), [IGVFFI0355RNEN](/sequence-files/IGVFFI0355RNEN/) 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/IGVFDS7378VQMR/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7378VQMR](/measurement-sets/IGVFDS7378VQMR/) has sequence file(s): [IGVFFI1833ZNCI](/sequence-files/IGVFFI1833ZNCI/), [IGVFFI5528AVXR](/sequence-files/IGVFFI5528AVXR/), [IGVFFI2338CLUZ](/sequence-files/IGVFFI2338CLUZ/), [IGVFFI1777GIOF](/sequence-files/IGVFFI1777GIOF/), [IGVFFI3872OVQC](/sequence-files/IGVFFI3872OVQC/), [IGVFFI2043WQOK](/sequence-files/IGVFFI2043WQOK/), [IGVFFI0826BDAP](/sequence-files/IGVFFI0826BDAP/), [IGVFFI0355RNEN](/sequence-files/IGVFFI0355RNEN/) 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/IGVFDS7378VQMR/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM2030BXGE](/in-vitro-systems/IGVFSM2030BXGE/) 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/IGVFSM2030BXGE/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS7378VQMR](/measurement-sets/IGVFDS7378VQMR/) 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/IGVFDS7378VQMR/"
}
]
},
"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": "2023-11-30T22:48:08.538669+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/IGVFFI1833ZNCI/",
"accession": "IGVFFI1833ZNCI",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinF-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:15:09.431466+00:00",
"file_format": "fastq",
"file_size": 15444552,
"href": "/sequence-files/IGVFFI1833ZNCI/@@download/IGVFFI1833ZNCI.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/2fd38d95-fa79-4547-b1f7-7248ed478803/IGVFFI1833ZNCI.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_S15-BioRep2-FFRep1-BinF-PCRrep2_S189_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5528AVXR/",
"accession": "IGVFFI5528AVXR",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinF-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:41:58.651362+00:00",
"file_format": "fastq",
"file_size": 13806999,
"href": "/sequence-files/IGVFFI5528AVXR/@@download/IGVFFI5528AVXR.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/ab6b0a0b-74f9-477d-b9e7-b0295c09a8fa/IGVFFI5528AVXR.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_S15-BioRep2-FFRep1-BinF-PCRrep1_S132_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2338CLUZ/",
"accession": "IGVFFI2338CLUZ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinF-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:31:53.805995+00:00",
"file_format": "fastq",
"file_size": 3420903,
"href": "/sequence-files/IGVFFI2338CLUZ/@@download/IGVFFI2338CLUZ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/69785a11-f00f-409a-8c81-fbc1877ca08a/IGVFFI2338CLUZ.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_S15-BioRep2-FFRep1-BinF-PCRrep2_S189_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1777GIOF/",
"accession": "IGVFFI1777GIOF",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinF-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:58:35.819719+00:00",
"file_format": "fastq",
"file_size": 3095544,
"href": "/sequence-files/IGVFFI1777GIOF/@@download/IGVFFI1777GIOF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/6f1b1f1f-8210-428f-879c-b8efa7a82007/IGVFFI1777GIOF.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_S15-BioRep2-FFRep1-BinF-PCRrep1_S132_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3872OVQC/",
"accession": "IGVFFI3872OVQC",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinF-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:23:33.333804+00:00",
"file_format": "fastq",
"file_size": 3600149,
"href": "/sequence-files/IGVFFI3872OVQC/@@download/IGVFFI3872OVQC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/32cf095c-ff6f-4164-ad22-bd4595e1332f/IGVFFI3872OVQC.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_S15-BioRep2-FFRep1-BinF-PCRrep2_S189_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2043WQOK/",
"accession": "IGVFFI2043WQOK",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinF-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:06:47.847797+00:00",
"file_format": "fastq",
"file_size": 8180310,
"href": "/sequence-files/IGVFFI2043WQOK/@@download/IGVFFI2043WQOK.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/732e827d-d988-4fd9-9bfe-3a4849536e63/IGVFFI2043WQOK.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_S15-BioRep2-FFRep1-BinF-PCRrep2_S189_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0826BDAP/",
"accession": "IGVFFI0826BDAP",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinF-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:50:28.557295+00:00",
"file_format": "fastq",
"file_size": 3141187,
"href": "/sequence-files/IGVFFI0826BDAP/@@download/IGVFFI0826BDAP.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/2d5b6c23-7a63-49ea-9023-e5a68a16536c/IGVFFI0826BDAP.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_S15-BioRep2-FFRep1-BinF-PCRrep1_S132_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0355RNEN/",
"accession": "IGVFFI0355RNEN",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinF-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:33:35.808279+00:00",
"file_format": "fastq",
"file_size": 7391296,
"href": "/sequence-files/IGVFFI0355RNEN/@@download/IGVFFI0355RNEN.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/6de37416-0bcb-4474-b212-d15c4107a73c/IGVFFI0355RNEN.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_S15-BioRep2-FFRep1-BinF-PCRrep1_S132_R1_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": "2023-12-20T23:03:55.153646+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2030BXGE/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2030BXGE",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinF"
],
"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 90-100% 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": "2023-12-05T19:33:35.808279+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": "deb210df-4837-4550-942d-9e39f498aa7d"
}