{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7615TALZ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7615TALZ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinE_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 [IGVFSM8221MKMD](/in-vitro-systems/IGVFSM8221MKMD/) 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/IGVFSM8221MKMD/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS7615TALZ](/measurement-sets/IGVFDS7615TALZ/) has sequence file(s) [IGVFFI1817KLHC](/sequence-files/IGVFFI1817KLHC/), [IGVFFI8173DFJI](/sequence-files/IGVFFI8173DFJI/), [IGVFFI3374PNLH](/sequence-files/IGVFFI3374PNLH/), [IGVFFI8117RKCN](/sequence-files/IGVFFI8117RKCN/), [IGVFFI4261TCEU](/sequence-files/IGVFFI4261TCEU/), [IGVFFI1965BSVQ](/sequence-files/IGVFFI1965BSVQ/), [IGVFFI0654UCFO](/sequence-files/IGVFFI0654UCFO/), [IGVFFI5538UAFA](/sequence-files/IGVFFI5538UAFA/) 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/IGVFDS7615TALZ/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7615TALZ](/measurement-sets/IGVFDS7615TALZ/) has sequence file(s): [IGVFFI1817KLHC](/sequence-files/IGVFFI1817KLHC/), [IGVFFI8173DFJI](/sequence-files/IGVFFI8173DFJI/), [IGVFFI3374PNLH](/sequence-files/IGVFFI3374PNLH/), [IGVFFI8117RKCN](/sequence-files/IGVFFI8117RKCN/), [IGVFFI4261TCEU](/sequence-files/IGVFFI4261TCEU/), [IGVFFI1965BSVQ](/sequence-files/IGVFFI1965BSVQ/), [IGVFFI0654UCFO](/sequence-files/IGVFFI0654UCFO/), [IGVFFI5538UAFA](/sequence-files/IGVFFI5538UAFA/) 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/IGVFDS7615TALZ/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS7615TALZ](/measurement-sets/IGVFDS7615TALZ/) 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/IGVFDS7615TALZ/"
}
]
},
"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": "2023-12-01T00:02:56.127952+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/IGVFFI1817KLHC/",
"accession": "IGVFFI1817KLHC",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinE-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:40:27.955998+00:00",
"file_format": "fastq",
"file_size": 7615764,
"href": "/sequence-files/IGVFFI1817KLHC/@@download/IGVFFI1817KLHC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/5f80cecb-f822-46d5-bdef-a9f8c748aade/IGVFFI1817KLHC.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_S2-BioRep1-FFRep1-BinE-PCRrep1_S5_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8173DFJI/",
"accession": "IGVFFI8173DFJI",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinE-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:25:04.503347+00:00",
"file_format": "fastq",
"file_size": 3081630,
"href": "/sequence-files/IGVFFI8173DFJI/@@download/IGVFFI8173DFJI.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/280163f2-62c9-4804-a377-ac41b4f70462/IGVFFI8173DFJI.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_S2-BioRep1-FFRep1-BinE-PCRrep2_S61_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3374PNLH/",
"accession": "IGVFFI3374PNLH",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinE-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:12:28.397773+00:00",
"file_format": "fastq",
"file_size": 3160481,
"href": "/sequence-files/IGVFFI3374PNLH/@@download/IGVFFI3374PNLH.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/47562893-1e5b-4875-85d7-3d5b768529c1/IGVFFI3374PNLH.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_S2-BioRep1-FFRep1-BinE-PCRrep2_S61_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8117RKCN/",
"accession": "IGVFFI8117RKCN",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinE-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:46:47.029156+00:00",
"file_format": "fastq",
"file_size": 7464041,
"href": "/sequence-files/IGVFFI8117RKCN/@@download/IGVFFI8117RKCN.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/f21944db-e31d-4393-89c9-85ee5874059e/IGVFFI8117RKCN.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_S2-BioRep1-FFRep1-BinE-PCRrep2_S61_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4261TCEU/",
"accession": "IGVFFI4261TCEU",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinE-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:06:15.054496+00:00",
"file_format": "fastq",
"file_size": 3243011,
"href": "/sequence-files/IGVFFI4261TCEU/@@download/IGVFFI4261TCEU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/38dcc812-0d2d-4e30-b3a4-c5c08e31979f/IGVFFI4261TCEU.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_S2-BioRep1-FFRep1-BinE-PCRrep1_S5_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1965BSVQ/",
"accession": "IGVFFI1965BSVQ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinE-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:59:39.429238+00:00",
"file_format": "fastq",
"file_size": 13687953,
"href": "/sequence-files/IGVFFI1965BSVQ/@@download/IGVFFI1965BSVQ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/ec3fde09-1b7c-4ce8-97ef-71094281f691/IGVFFI1965BSVQ.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_S2-BioRep1-FFRep1-BinE-PCRrep2_S61_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0654UCFO/",
"accession": "IGVFFI0654UCFO",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinE-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:18:43.376217+00:00",
"file_format": "fastq",
"file_size": 3124469,
"href": "/sequence-files/IGVFFI0654UCFO/@@download/IGVFFI0654UCFO.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/24a6275e-efa9-4a39-835b-7fce4e469cfc/IGVFFI0654UCFO.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_S2-BioRep1-FFRep1-BinE-PCRrep1_S5_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5538UAFA/",
"accession": "IGVFFI5538UAFA",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinE-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:53:06.781506+00:00",
"file_format": "fastq",
"file_size": 13913385,
"href": "/sequence-files/IGVFFI5538UAFA/@@download/IGVFFI5538UAFA.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/29448571-7556-486e-8f99-bb83d17a73c8/IGVFFI5538UAFA.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_S2-BioRep1-FFRep1-BinE-PCRrep1_S5_R2_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": "2023-12-20T23:04:32.071369+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8221MKMD/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8221MKMD",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinE"
],
"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 80-90% 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": "2023-12-05T18:40:27.955998+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": "19f6be30-87a4-4270-b270-ec15d026f67a"
}