{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5918LGHY/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5918LGHY",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep2-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 [IGVFDS5918LGHY](/measurement-sets/IGVFDS5918LGHY/) has sequence file(s) [IGVFFI7427IFEY](/sequence-files/IGVFFI7427IFEY/), [IGVFFI8343RFNF](/sequence-files/IGVFFI8343RFNF/), [IGVFFI2356UHQX](/sequence-files/IGVFFI2356UHQX/), [IGVFFI1115NAIR](/sequence-files/IGVFFI1115NAIR/), [IGVFFI0332UTBX](/sequence-files/IGVFFI0332UTBX/), [IGVFFI8886YNSM](/sequence-files/IGVFFI8886YNSM/), [IGVFFI5845WQIZ](/sequence-files/IGVFFI5845WQIZ/), [IGVFFI6182EUIW](/sequence-files/IGVFFI6182EUIW/) 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/IGVFDS5918LGHY/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS5918LGHY](/measurement-sets/IGVFDS5918LGHY/) has sequence file(s): [IGVFFI7427IFEY](/sequence-files/IGVFFI7427IFEY/), [IGVFFI8343RFNF](/sequence-files/IGVFFI8343RFNF/), [IGVFFI2356UHQX](/sequence-files/IGVFFI2356UHQX/), [IGVFFI1115NAIR](/sequence-files/IGVFFI1115NAIR/), [IGVFFI0332UTBX](/sequence-files/IGVFFI0332UTBX/), [IGVFFI8886YNSM](/sequence-files/IGVFFI8886YNSM/), [IGVFFI5845WQIZ](/sequence-files/IGVFFI5845WQIZ/), [IGVFFI6182EUIW](/sequence-files/IGVFFI6182EUIW/) 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/IGVFDS5918LGHY/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM1022AFZT](/in-vitro-systems/IGVFSM1022AFZT/) 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/IGVFSM1022AFZT/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS5918LGHY](/measurement-sets/IGVFDS5918LGHY/) 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/IGVFDS5918LGHY/"
}
]
},
"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": "2023-11-30T22:48:46.402633+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": [
{
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"accession": "IGVFFI7427IFEY",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep2-BinF-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:03:40.455762+00:00",
"file_format": "fastq",
"file_size": 3246801,
"href": "/sequence-files/IGVFFI7427IFEY/@@download/IGVFFI7427IFEY.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/3c45e8f6-fd15-4114-8cd9-581751d53308/IGVFFI7427IFEY.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_S20-BioRep4-FFRep2-BinF-PCRrep1_S167_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8343RFNF/",
"accession": "IGVFFI8343RFNF",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep2-BinF-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:36:59.864592+00:00",
"file_format": "fastq",
"file_size": 3126343,
"href": "/sequence-files/IGVFFI8343RFNF/@@download/IGVFFI8343RFNF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/9514c434-a8b2-4869-bbec-047670172fc7/IGVFFI8343RFNF.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_S20-BioRep4-FFRep2-BinF-PCRrep2_S224_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2356UHQX/",
"accession": "IGVFFI2356UHQX",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep2-BinF-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:38:46.431736+00:00",
"file_format": "fastq",
"file_size": 7723917,
"href": "/sequence-files/IGVFFI2356UHQX/@@download/IGVFFI2356UHQX.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/4b066e17-f28d-4342-8b81-3f9ebd6b31fa/IGVFFI2356UHQX.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_S20-BioRep4-FFRep2-BinF-PCRrep1_S167_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1115NAIR/",
"accession": "IGVFFI1115NAIR",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep2-BinF-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:20:29.744879+00:00",
"file_format": "fastq",
"file_size": 13990946,
"href": "/sequence-files/IGVFFI1115NAIR/@@download/IGVFFI1115NAIR.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/f2ce6e90-56c3-445e-921b-0929e3accc56/IGVFFI1115NAIR.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_S20-BioRep4-FFRep2-BinF-PCRrep2_S224_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0332UTBX/",
"accession": "IGVFFI0332UTBX",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep2-BinF-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:28:47.213238+00:00",
"file_format": "fastq",
"file_size": 3081685,
"href": "/sequence-files/IGVFFI0332UTBX/@@download/IGVFFI0332UTBX.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/378ffa14-7360-4c3b-851d-0d1ab2b2b877/IGVFFI0332UTBX.fastq.gz",
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"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S20-BioRep4-FFRep2-BinF-PCRrep2_S224_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8886YNSM/",
"accession": "IGVFFI8886YNSM",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep2-BinF-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:11:57.608189+00:00",
"file_format": "fastq",
"file_size": 7419236,
"href": "/sequence-files/IGVFFI8886YNSM/@@download/IGVFFI8886YNSM.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/a8e3776e-f230-49b5-8af6-d9a8ce888b18/IGVFFI8886YNSM.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_S20-BioRep4-FFRep2-BinF-PCRrep2_S224_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5845WQIZ/",
"accession": "IGVFFI5845WQIZ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep2-BinF-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:55:33.368910+00:00",
"file_format": "fastq",
"file_size": 3352924,
"href": "/sequence-files/IGVFFI5845WQIZ/@@download/IGVFFI5845WQIZ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/26e57a9b-18a1-4dcd-a848-5d337adca94c/IGVFFI5845WQIZ.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_S20-BioRep4-FFRep2-BinF-PCRrep1_S167_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6182EUIW/",
"accession": "IGVFFI6182EUIW",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep2-BinF-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:47:18.983303+00:00",
"file_format": "fastq",
"file_size": 14444361,
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"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_S20-BioRep4-FFRep2-BinF-PCRrep1_S167_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": "2023-12-20T23:10:37.197327+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1022AFZT/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1022AFZT",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep2-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": "2023-12-05T19:38:46.431736+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": "eab77d47-013c-4bf1-a362-03b5007b6630"
}