{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1892KLOO/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1892KLOO",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep2-BinA_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 [IGVFSM1944NSGS](/in-vitro-systems/IGVFSM1944NSGS/) 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/IGVFSM1944NSGS/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS1892KLOO](/measurement-sets/IGVFDS1892KLOO/) has sequence file(s) [IGVFFI7227ZYVR](/sequence-files/IGVFFI7227ZYVR/), [IGVFFI6740WDWS](/sequence-files/IGVFFI6740WDWS/), [IGVFFI7748BVLU](/sequence-files/IGVFFI7748BVLU/), [IGVFFI8219JGAN](/sequence-files/IGVFFI8219JGAN/), [IGVFFI7167SWNF](/sequence-files/IGVFFI7167SWNF/), [IGVFFI9799BCEM](/sequence-files/IGVFFI9799BCEM/), [IGVFFI5000GUXW](/sequence-files/IGVFFI5000GUXW/), [IGVFFI5526TZOW](/sequence-files/IGVFFI5526TZOW/) 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/IGVFDS1892KLOO/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS1892KLOO](/measurement-sets/IGVFDS1892KLOO/) has sequence file(s): [IGVFFI7227ZYVR](/sequence-files/IGVFFI7227ZYVR/), [IGVFFI6740WDWS](/sequence-files/IGVFFI6740WDWS/), [IGVFFI7748BVLU](/sequence-files/IGVFFI7748BVLU/), [IGVFFI8219JGAN](/sequence-files/IGVFFI8219JGAN/), [IGVFFI7167SWNF](/sequence-files/IGVFFI7167SWNF/), [IGVFFI9799BCEM](/sequence-files/IGVFFI9799BCEM/), [IGVFFI5000GUXW](/sequence-files/IGVFFI5000GUXW/), [IGVFFI5526TZOW](/sequence-files/IGVFFI5526TZOW/) 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/IGVFDS1892KLOO/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS1892KLOO](/measurement-sets/IGVFDS1892KLOO/) 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/IGVFDS1892KLOO/"
}
]
},
"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": "2023-11-30T22:48:39.881100+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/IGVFFI7227ZYVR/",
"accession": "IGVFFI7227ZYVR",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep2-BinA-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:11:13.314104+00:00",
"file_format": "fastq",
"file_size": 7933041,
"href": "/sequence-files/IGVFFI7227ZYVR/@@download/IGVFFI7227ZYVR.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/0e377eed-9dd2-44b9-8832-26e6bc22d73f/IGVFFI7227ZYVR.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-BinA-PCRrep2_S219_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6740WDWS/",
"accession": "IGVFFI6740WDWS",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep2-BinA-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:28:03.592630+00:00",
"file_format": "fastq",
"file_size": 3339849,
"href": "/sequence-files/IGVFFI6740WDWS/@@download/IGVFFI6740WDWS.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/b8a99898-e28d-48c2-92e4-e60c065efaab/IGVFFI6740WDWS.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-BinA-PCRrep2_S219_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7748BVLU/",
"accession": "IGVFFI7748BVLU",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep2-BinA-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:54:49.968161+00:00",
"file_format": "fastq",
"file_size": 3561147,
"href": "/sequence-files/IGVFFI7748BVLU/@@download/IGVFFI7748BVLU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/beba6920-d488-485c-b8c7-e770b381595c/IGVFFI7748BVLU.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-BinA-PCRrep1_S162_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8219JGAN/",
"accession": "IGVFFI8219JGAN",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep2-BinA-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:38:01.697967+00:00",
"file_format": "fastq",
"file_size": 8157343,
"href": "/sequence-files/IGVFFI8219JGAN/@@download/IGVFFI8219JGAN.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/453dc182-c098-4b3c-8499-3df2f98d45fb/IGVFFI8219JGAN.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-BinA-PCRrep1_S162_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7167SWNF/",
"accession": "IGVFFI7167SWNF",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep2-BinA-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:36:16.419040+00:00",
"file_format": "fastq",
"file_size": 3323967,
"href": "/sequence-files/IGVFFI7167SWNF/@@download/IGVFFI7167SWNF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/d60d7f45-167d-4f8f-b7c0-538275b7b770/IGVFFI7167SWNF.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-BinA-PCRrep2_S219_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9799BCEM/",
"accession": "IGVFFI9799BCEM",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep2-BinA-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:46:32.953568+00:00",
"file_format": "fastq",
"file_size": 14756210,
"href": "/sequence-files/IGVFFI9799BCEM/@@download/IGVFFI9799BCEM.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/819feea7-d7a4-410d-9788-708bff296786/IGVFFI9799BCEM.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-BinA-PCRrep1_S162_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5000GUXW/",
"accession": "IGVFFI5000GUXW",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep2-BinA-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:02:57.010357+00:00",
"file_format": "fastq",
"file_size": 3367636,
"href": "/sequence-files/IGVFFI5000GUXW/@@download/IGVFFI5000GUXW.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/f77d0823-9b7e-4a35-a05b-fa16ed413f49/IGVFFI5000GUXW.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-BinA-PCRrep1_S162_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5526TZOW/",
"accession": "IGVFFI5526TZOW",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep2-BinA-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:19:44.007480+00:00",
"file_format": "fastq",
"file_size": 14607437,
"href": "/sequence-files/IGVFFI5526TZOW/@@download/IGVFFI5526TZOW.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/c77d8e72-8b0b-458d-8a9e-c296f2c0a1c9/IGVFFI5526TZOW.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-BinA-PCRrep2_S219_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": "2023-12-20T23:11:08.483552+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1944NSGS/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1944NSGS",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep2-BinA"
],
"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 0-10% 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": "2023-12-05T19:38:01.697967+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": "35ea9fa0-d5b6-4217-ab01-2412bee56531"
}