{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1677ZRBK/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1677ZRBK",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinD_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 [IGVFDS1677ZRBK](/measurement-sets/IGVFDS1677ZRBK/) has sequence file(s) [IGVFFI1923TIFY](/sequence-files/IGVFFI1923TIFY/), [IGVFFI8766DBQI](/sequence-files/IGVFFI8766DBQI/), [IGVFFI8153OVYR](/sequence-files/IGVFFI8153OVYR/), [IGVFFI0657VNCY](/sequence-files/IGVFFI0657VNCY/), [IGVFFI3647KUPH](/sequence-files/IGVFFI3647KUPH/), [IGVFFI9724RAQD](/sequence-files/IGVFFI9724RAQD/), [IGVFFI4971OSYC](/sequence-files/IGVFFI4971OSYC/), [IGVFFI0533QMYX](/sequence-files/IGVFFI0533QMYX/) 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/IGVFDS1677ZRBK/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS1677ZRBK](/measurement-sets/IGVFDS1677ZRBK/) has sequence file(s): [IGVFFI1923TIFY](/sequence-files/IGVFFI1923TIFY/), [IGVFFI8766DBQI](/sequence-files/IGVFFI8766DBQI/), [IGVFFI8153OVYR](/sequence-files/IGVFFI8153OVYR/), [IGVFFI0657VNCY](/sequence-files/IGVFFI0657VNCY/), [IGVFFI3647KUPH](/sequence-files/IGVFFI3647KUPH/), [IGVFFI9724RAQD](/sequence-files/IGVFFI9724RAQD/), [IGVFFI4971OSYC](/sequence-files/IGVFFI4971OSYC/), [IGVFFI0533QMYX](/sequence-files/IGVFFI0533QMYX/) 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/IGVFDS1677ZRBK/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM3934QVMQ](/in-vitro-systems/IGVFSM3934QVMQ/) 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/IGVFSM3934QVMQ/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS1677ZRBK](/measurement-sets/IGVFDS1677ZRBK/) 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/IGVFDS1677ZRBK/"
}
]
},
"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": "2023-11-30T22:47:19.076690+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": "IGVFFI1923TIFY",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinD-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:20:37.177508+00:00",
"file_format": "fastq",
"file_size": 2980431,
"href": "/sequence-files/IGVFFI1923TIFY/@@download/IGVFFI1923TIFY.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/87f5bea9-8c99-4e45-b623-9dabc45af6ad/IGVFFI1923TIFY.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_S5-BioRep2-FFRep1-BinD-PCRrep1_S18_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8766DBQI/",
"accession": "IGVFFI8766DBQI",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinD-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:42:22.857184+00:00",
"file_format": "fastq",
"file_size": 7201488,
"href": "/sequence-files/IGVFFI8766DBQI/@@download/IGVFFI8766DBQI.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/66063956-cb4f-462c-8813-c2294f8862eb/IGVFFI8766DBQI.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_S5-BioRep2-FFRep1-BinD-PCRrep1_S18_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8153OVYR/",
"accession": "IGVFFI8153OVYR",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinD-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:26:57.257304+00:00",
"file_format": "fastq",
"file_size": 3020228,
"href": "/sequence-files/IGVFFI8153OVYR/@@download/IGVFFI8153OVYR.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/ca5075b1-7bf2-4ba6-ac2e-039415116dae/IGVFFI8153OVYR.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_S5-BioRep2-FFRep1-BinD-PCRrep2_S74_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0657VNCY/",
"accession": "IGVFFI0657VNCY",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinD-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:14:21.904839+00:00",
"file_format": "fastq",
"file_size": 3225592,
"href": "/sequence-files/IGVFFI0657VNCY/@@download/IGVFFI0657VNCY.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/296216fd-7be5-4969-875a-0d820c49fadd/IGVFFI0657VNCY.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_S5-BioRep2-FFRep1-BinD-PCRrep2_S74_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3647KUPH/",
"accession": "IGVFFI3647KUPH",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinD-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:08:06.446460+00:00",
"file_format": "fastq",
"file_size": 3181308,
"href": "/sequence-files/IGVFFI3647KUPH/@@download/IGVFFI3647KUPH.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/68f56c18-be60-409e-84b0-21d2a811c8f7/IGVFFI3647KUPH.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_S5-BioRep2-FFRep1-BinD-PCRrep1_S18_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9724RAQD/",
"accession": "IGVFFI9724RAQD",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinD-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:55:05.267519+00:00",
"file_format": "fastq",
"file_size": 13205970,
"href": "/sequence-files/IGVFFI9724RAQD/@@download/IGVFFI9724RAQD.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/4a184bb7-46d8-4319-bc47-777dce588fe1/IGVFFI9724RAQD.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_S5-BioRep2-FFRep1-BinD-PCRrep1_S18_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4971OSYC/",
"accession": "IGVFFI4971OSYC",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinD-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:01:42.967395+00:00",
"file_format": "fastq",
"file_size": 13509211,
"href": "/sequence-files/IGVFFI4971OSYC/@@download/IGVFFI4971OSYC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/07986435-c7fe-4c83-886b-e912902320e4/IGVFFI4971OSYC.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_S5-BioRep2-FFRep1-BinD-PCRrep2_S74_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0533QMYX/",
"accession": "IGVFFI0533QMYX",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinD-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:48:41.393756+00:00",
"file_format": "fastq",
"file_size": 7323070,
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"s3_uri": "s3://igvf-files/2023/12/05/ee2a47ae-e202-446c-aca8-2ffa511bffbe/IGVFFI0533QMYX.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_S5-BioRep2-FFRep1-BinD-PCRrep2_S74_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": "2023-12-20T23:04:34.564844+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3934QVMQ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3934QVMQ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-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": "2023-12-05T18:42:22.857184+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": "73dc03aa-a06c-4232-95b5-95ce73e7943e"
}