{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0329UHSG/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0329UHSG",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinA_AmpliconSequencing"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"assay_slims": [
"CRISPR screens"
],
"status": "released",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS0329UHSG](/measurement-sets/IGVFDS0329UHSG/) has sequence file(s) [IGVFFI8058IJZH](/sequence-files/IGVFFI8058IJZH/), [IGVFFI1689MKOK](/sequence-files/IGVFFI1689MKOK/), [IGVFFI2015TTTJ](/sequence-files/IGVFFI2015TTTJ/), [IGVFFI6068UEFK](/sequence-files/IGVFFI6068UEFK/), [IGVFFI6632LIMD](/sequence-files/IGVFFI6632LIMD/), [IGVFFI7530SUEE](/sequence-files/IGVFFI7530SUEE/), [IGVFFI1869QKXY](/sequence-files/IGVFFI1869QKXY/), [IGVFFI6252FOFU](/sequence-files/IGVFFI6252FOFU/) which lack specification of a `sequencing_kit`. Sequence files in a file set associated wtih bulk data should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/measurement-sets/IGVFDS0329UHSG/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS0329UHSG](/measurement-sets/IGVFDS0329UHSG/) has sequence file(s): [IGVFFI8058IJZH](/sequence-files/IGVFFI8058IJZH/), [IGVFFI1689MKOK](/sequence-files/IGVFFI1689MKOK/), [IGVFFI2015TTTJ](/sequence-files/IGVFFI2015TTTJ/), [IGVFFI6068UEFK](/sequence-files/IGVFFI6068UEFK/), [IGVFFI6632LIMD](/sequence-files/IGVFFI6632LIMD/), [IGVFFI7530SUEE](/sequence-files/IGVFFI7530SUEE/), [IGVFFI1869QKXY](/sequence-files/IGVFFI1869QKXY/), [IGVFFI6252FOFU](/sequence-files/IGVFFI6252FOFU/) which do not have any `seqspecs`. Sequence files in a file set associated with bulk data are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS0329UHSG/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM9398KLPK](/in-vitro-systems/IGVFSM9398KLPK/) 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/IGVFSM9398KLPK/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS0329UHSG](/measurement-sets/IGVFDS0329UHSG/) 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/IGVFDS0329UHSG/"
},
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM9398KLPK](/in-vitro-systems/IGVFSM9398KLPK/) has `construct_library_sets` but is missing `nucleic_acid_delivery`. Samples linked to construct library sets are expected to specify nucleic acid delivery method.",
"level": 40,
"level_name": "WARNING",
"name": "audit_missing_nucleic_acid_delivery",
"path": "/in-vitro-systems/IGVFSM9398KLPK/"
}
]
},
"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"
},
"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"
}
],
"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": "2023-11-30T22:47:30.261281+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/IGVFFI8058IJZH/",
"accession": "IGVFFI8058IJZH",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinA-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:50:18.096467+00:00",
"file_format": "fastq",
"file_size": 7761331,
"href": "/sequence-files/IGVFFI8058IJZH/@@download/IGVFFI8058IJZH.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/5238b528-47c5-47b3-82ef-cef9f4d00812/IGVFFI8058IJZH.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_S7-BioRep3-FFRep1-BinA-PCRrep2_S85_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1689MKOK/",
"accession": "IGVFFI1689MKOK",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinA-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:15:58.018277+00:00",
"file_format": "fastq",
"file_size": 3218669,
"href": "/sequence-files/IGVFFI1689MKOK/@@download/IGVFFI1689MKOK.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/890925ec-ae7e-49a2-a9e9-4f6979ba98b7/IGVFFI1689MKOK.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_S7-BioRep3-FFRep1-BinA-PCRrep2_S85_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2015TTTJ/",
"accession": "IGVFFI2015TTTJ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinA-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:43:59.204136+00:00",
"file_format": "fastq",
"file_size": 7066929,
"href": "/sequence-files/IGVFFI2015TTTJ/@@download/IGVFFI2015TTTJ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/9386255a-804f-4438-8b0a-df345a306049/IGVFFI2015TTTJ.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_S7-BioRep3-FFRep1-BinA-PCRrep1_S29_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6068UEFK/",
"accession": "IGVFFI6068UEFK",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinA-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:22:14.662491+00:00",
"file_format": "fastq",
"file_size": 2897849,
"href": "/sequence-files/IGVFFI6068UEFK/@@download/IGVFFI6068UEFK.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/20ef4a8b-72b7-4b0e-975a-28dde55df88c/IGVFFI6068UEFK.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_S7-BioRep3-FFRep1-BinA-PCRrep1_S29_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6632LIMD/",
"accession": "IGVFFI6632LIMD",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinA-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:28:33.654314+00:00",
"file_format": "fastq",
"file_size": 3151947,
"href": "/sequence-files/IGVFFI6632LIMD/@@download/IGVFFI6632LIMD.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/68746296-cae3-4676-9cec-9210c8b4522f/IGVFFI6632LIMD.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_S7-BioRep3-FFRep1-BinA-PCRrep2_S85_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7530SUEE/",
"accession": "IGVFFI7530SUEE",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinA-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:03:22.888474+00:00",
"file_format": "fastq",
"file_size": 14083616,
"href": "/sequence-files/IGVFFI7530SUEE/@@download/IGVFFI7530SUEE.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/aebcf63f-30ff-4410-8287-0aac868f90e4/IGVFFI7530SUEE.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_S7-BioRep3-FFRep1-BinA-PCRrep2_S85_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1869QKXY/",
"accession": "IGVFFI1869QKXY",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinA-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:09:42.548668+00:00",
"file_format": "fastq",
"file_size": 3231751,
"href": "/sequence-files/IGVFFI1869QKXY/@@download/IGVFFI1869QKXY.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/fdbfbbff-e733-427f-8551-b4d4908a5fad/IGVFFI1869QKXY.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_S7-BioRep3-FFRep1-BinA-PCRrep1_S29_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6252FOFU/",
"accession": "IGVFFI6252FOFU",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinA-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:56:45.900881+00:00",
"file_format": "fastq",
"file_size": 12921148,
"href": "/sequence-files/IGVFFI6252FOFU/@@download/IGVFFI6252FOFU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/1696aa83-35cb-40a7-b706-852163bad96f/IGVFFI6252FOFU.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_S7-BioRep3-FFRep1-BinA-PCRrep1_S29_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": "2023-12-20T23:04:40.853030+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9398KLPK/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9398KLPK",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinA"
],
"classifications": [
"cell line"
],
"institutional_certificates": [],
"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 0-10% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transfected with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "25",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T18:43:59.204136+00:00",
"summary": "CRISPR prime editing Variant-EFFECTS sorted on the expression of PPIF 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": "44dc3d34-c896-4171-ba4f-c1a273787cf1"
}