{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4690FWJW/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4690FWJW",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinD_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 [IGVFSM2667WDHP](/in-vitro-systems/IGVFSM2667WDHP/) 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/IGVFSM2667WDHP/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS4690FWJW](/measurement-sets/IGVFDS4690FWJW/) has sequence file(s) [IGVFFI2418WHMY](/sequence-files/IGVFFI2418WHMY/), [IGVFFI9327GSHM](/sequence-files/IGVFFI9327GSHM/), [IGVFFI4071WYUI](/sequence-files/IGVFFI4071WYUI/), [IGVFFI6079JRIZ](/sequence-files/IGVFFI6079JRIZ/), [IGVFFI5357WIRO](/sequence-files/IGVFFI5357WIRO/), [IGVFFI2414KEEU](/sequence-files/IGVFFI2414KEEU/), [IGVFFI2694QPZZ](/sequence-files/IGVFFI2694QPZZ/), [IGVFFI3599ALAA](/sequence-files/IGVFFI3599ALAA/) 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/IGVFDS4690FWJW/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS4690FWJW](/measurement-sets/IGVFDS4690FWJW/) has sequence file(s): [IGVFFI2418WHMY](/sequence-files/IGVFFI2418WHMY/), [IGVFFI9327GSHM](/sequence-files/IGVFFI9327GSHM/), [IGVFFI4071WYUI](/sequence-files/IGVFFI4071WYUI/), [IGVFFI6079JRIZ](/sequence-files/IGVFFI6079JRIZ/), [IGVFFI5357WIRO](/sequence-files/IGVFFI5357WIRO/), [IGVFFI2414KEEU](/sequence-files/IGVFFI2414KEEU/), [IGVFFI2694QPZZ](/sequence-files/IGVFFI2694QPZZ/), [IGVFFI3599ALAA](/sequence-files/IGVFFI3599ALAA/) 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/IGVFDS4690FWJW/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS4690FWJW](/measurement-sets/IGVFDS4690FWJW/) 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/IGVFDS4690FWJW/"
}
]
},
"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": "2023-11-30T22:47:42.315486+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/IGVFFI2418WHMY/",
"accession": "IGVFFI2418WHMY",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinD-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:30:00.636835+00:00",
"file_format": "fastq",
"file_size": 3429450,
"href": "/sequence-files/IGVFFI2418WHMY/@@download/IGVFFI2418WHMY.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/5151b7ab-ea42-4080-9fc2-3cdf589dca7f/IGVFFI2418WHMY.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_S8-BioRep3-FFRep2-BinD-PCRrep2_S95_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9327GSHM/",
"accession": "IGVFFI9327GSHM",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinD-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:17:25.258199+00:00",
"file_format": "fastq",
"file_size": 3499588,
"href": "/sequence-files/IGVFFI9327GSHM/@@download/IGVFFI9327GSHM.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/60dfd8de-6438-4726-b4f8-bae049cc34f5/IGVFFI9327GSHM.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_S8-BioRep3-FFRep2-BinD-PCRrep2_S95_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4071WYUI/",
"accession": "IGVFFI4071WYUI",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinD-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:45:27.970362+00:00",
"file_format": "fastq",
"file_size": 7639565,
"href": "/sequence-files/IGVFFI4071WYUI/@@download/IGVFFI4071WYUI.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/2ed0c5c1-c9ab-422d-906e-a61279788331/IGVFFI4071WYUI.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_S8-BioRep3-FFRep2-BinD-PCRrep1_S39_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6079JRIZ/",
"accession": "IGVFFI6079JRIZ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinD-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:11:09.607372+00:00",
"file_format": "fastq",
"file_size": 3189298,
"href": "/sequence-files/IGVFFI6079JRIZ/@@download/IGVFFI6079JRIZ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/fb0f035c-c155-4277-a949-b289aae5d620/IGVFFI6079JRIZ.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_S8-BioRep3-FFRep2-BinD-PCRrep1_S39_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5357WIRO/",
"accession": "IGVFFI5357WIRO",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinD-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:04:54.531378+00:00",
"file_format": "fastq",
"file_size": 15262266,
"href": "/sequence-files/IGVFFI5357WIRO/@@download/IGVFFI5357WIRO.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/79967400-62d0-4454-9b1d-de722d34ab63/IGVFFI5357WIRO.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_pPPIF_S8-BioRep3-FFRep2-BinD-PCRrep2_S95_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2414KEEU/",
"accession": "IGVFFI2414KEEU",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinD-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:23:45.673053+00:00",
"file_format": "fastq",
"file_size": 3148668,
"href": "/sequence-files/IGVFFI2414KEEU/@@download/IGVFFI2414KEEU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/e60a0fe6-d00c-4426-b9f4-aff4929ff7b0/IGVFFI2414KEEU.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_S8-BioRep3-FFRep2-BinD-PCRrep1_S39_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2694QPZZ/",
"accession": "IGVFFI2694QPZZ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinD-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:58:17.033430+00:00",
"file_format": "fastq",
"file_size": 13955144,
"href": "/sequence-files/IGVFFI2694QPZZ/@@download/IGVFFI2694QPZZ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/2c9cced2-6722-4c36-a31a-d11d1be6e336/IGVFFI2694QPZZ.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_pPPIF_S8-BioRep3-FFRep2-BinD-PCRrep1_S39_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3599ALAA/",
"accession": "IGVFFI3599ALAA",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinD-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:51:45.802096+00:00",
"file_format": "fastq",
"file_size": 8245720,
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"s3_uri": "s3://igvf-files/2023/12/05/f725694d-efe8-4b6a-92ca-3509a9428f8b/IGVFFI3599ALAA.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_pPPIF_S8-BioRep3-FFRep2-BinD-PCRrep2_S95_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": "2023-12-20T23:05:07.966654+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2667WDHP/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2667WDHP",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinD"
],
"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 55-65% 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": "2023-12-05T18:45:27.970362+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": "7e52c0b4-bd25-41d4-a9c0-aa14440d246a"
}