{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0892KCXO/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0892KCXO",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinB_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": "mismatched status",
"detail": "Released in vitro system [IGVFSM2054NOCA](/in-vitro-systems/IGVFSM2054NOCA/) 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/IGVFSM2054NOCA/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM2054NOCA](/in-vitro-systems/IGVFSM2054NOCA/) has no `publications`. Released and archived samples are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_sample_missing_publication",
"path": "/in-vitro-systems/IGVFSM2054NOCA/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS0892KCXO](/measurement-sets/IGVFDS0892KCXO/) has no `publications`. Released and archived file sets are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_file_set_missing_publication",
"path": "/measurement-sets/IGVFDS0892KCXO/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS0892KCXO](/measurement-sets/IGVFDS0892KCXO/) has sequence file(s) [IGVFFI8723DODK](/sequence-files/IGVFFI8723DODK/), [IGVFFI3015OMYP](/sequence-files/IGVFFI3015OMYP/), [IGVFFI0060HNZK](/sequence-files/IGVFFI0060HNZK/), [IGVFFI2400EHXK](/sequence-files/IGVFFI2400EHXK/), [IGVFFI1523LWBS](/sequence-files/IGVFFI1523LWBS/), [IGVFFI9260XIIP](/sequence-files/IGVFFI9260XIIP/), [IGVFFI0516IWYG](/sequence-files/IGVFFI0516IWYG/), [IGVFFI5531YTVF](/sequence-files/IGVFFI5531YTVF/) 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/IGVFDS0892KCXO/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS0892KCXO](/measurement-sets/IGVFDS0892KCXO/) has sequence file(s): [IGVFFI8723DODK](/sequence-files/IGVFFI8723DODK/), [IGVFFI3015OMYP](/sequence-files/IGVFFI3015OMYP/), [IGVFFI0060HNZK](/sequence-files/IGVFFI0060HNZK/), [IGVFFI2400EHXK](/sequence-files/IGVFFI2400EHXK/), [IGVFFI1523LWBS](/sequence-files/IGVFFI1523LWBS/), [IGVFFI9260XIIP](/sequence-files/IGVFFI9260XIIP/), [IGVFFI0516IWYG](/sequence-files/IGVFFI0516IWYG/), [IGVFFI5531YTVF](/sequence-files/IGVFFI5531YTVF/) 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/IGVFDS0892KCXO/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS0892KCXO](/measurement-sets/IGVFDS0892KCXO/) 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/IGVFDS0892KCXO/"
}
]
},
"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": "2023-11-30T22:47:55.678899+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": "IGVFFI8723DODK",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:05:08.958979+00:00",
"file_format": "fastq",
"file_size": 7534890,
"href": "/sequence-files/IGVFFI8723DODK/@@download/IGVFFI8723DODK.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/b3c1b622-1cb8-47b4-9239-456ebb68af84/IGVFFI8723DODK.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_S13-BioRep1-FFRep2-BinB-PCRrep2_S178_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3015OMYP/",
"accession": "IGVFFI3015OMYP",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinB-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:30:17.956678+00:00",
"file_format": "fastq",
"file_size": 3132057,
"href": "/sequence-files/IGVFFI3015OMYP/@@download/IGVFFI3015OMYP.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/c26b2333-2269-4f64-aa87-d0dcc9d69670/IGVFFI3015OMYP.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_S13-BioRep1-FFRep2-BinB-PCRrep2_S178_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0060HNZK/",
"accession": "IGVFFI0060HNZK",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinB-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:31:55.193121+00:00",
"file_format": "fastq",
"file_size": 7005241,
"href": "/sequence-files/IGVFFI0060HNZK/@@download/IGVFFI0060HNZK.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/50334b2c-10aa-475a-9738-84e9d90c3863/IGVFFI0060HNZK.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_S13-BioRep1-FFRep2-BinB-PCRrep1_S121_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2400EHXK/",
"accession": "IGVFFI2400EHXK",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinB-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:21:57.615311+00:00",
"file_format": "fastq",
"file_size": 3291478,
"href": "/sequence-files/IGVFFI2400EHXK/@@download/IGVFFI2400EHXK.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/9f67029d-8c15-450b-b92f-e13f220dac3a/IGVFFI2400EHXK.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_S13-BioRep1-FFRep2-BinB-PCRrep2_S178_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1523LWBS/",
"accession": "IGVFFI1523LWBS",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinB-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:57:00.151756+00:00",
"file_format": "fastq",
"file_size": 2920057,
"href": "/sequence-files/IGVFFI1523LWBS/@@download/IGVFFI1523LWBS.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/2df332e9-5ec0-4c95-a5b1-93c40c7016b1/IGVFFI1523LWBS.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_S13-BioRep1-FFRep2-BinB-PCRrep1_S121_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9260XIIP/",
"accession": "IGVFFI9260XIIP",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinB-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:48:52.473598+00:00",
"file_format": "fastq",
"file_size": 2979370,
"href": "/sequence-files/IGVFFI9260XIIP/@@download/IGVFFI9260XIIP.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/fd33187e-1d5a-41cf-b2a7-0b57ae76ea87/IGVFFI9260XIIP.fastq.gz",
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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_S13-BioRep1-FFRep2-BinB-PCRrep1_S121_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0516IWYG/",
"accession": "IGVFFI0516IWYG",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinB-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:40:17.678344+00:00",
"file_format": "fastq",
"file_size": 12802631,
"href": "/sequence-files/IGVFFI0516IWYG/@@download/IGVFFI0516IWYG.fastq.gz",
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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_S13-BioRep1-FFRep2-BinB-PCRrep1_S121_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5531YTVF/",
"accession": "IGVFFI5531YTVF",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinB-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:13:28.175318+00:00",
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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_S13-BioRep1-FFRep2-BinB-PCRrep2_S178_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": "2023-12-20T23:10:53.369053+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2054NOCA/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2054NOCA",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinB"
],
"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": "Homo sapiens (male) Jurkat cell line (sorting details: FACS bin for 11-20% 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), transduced (lentivirus) with a guide library",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/df02c0d4-f796-4f77-bfbc-388cdbfcc615/",
"purpose": "stimulation",
"status": "released",
"summary": "Treatment of 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 4 hours",
"treatment_type": "protein"
},
{
"@id": "/treatments/42b3c61d-38de-4bd2-bb39-33c125a417cb/",
"purpose": "stimulation",
"status": "released",
"summary": "Treatment of 100 ng/mL phorbol 13-acetate 12-myristate for 4 hours",
"treatment_type": "chemical"
}
]
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T19:31:55.193121+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": [
"PPIase F",
"peptidylprolyl isomerase F",
"Cyp-D",
"peptidyl-prolyl cis-trans isomerase F, mitochondrial",
"PPIF",
"CyP-M",
"cyclophilin F",
"peptidyl-prolyl cis-trans isomerase, mitochondrial",
"cyclophilin 3",
"cyclophilin D",
"rotamase F",
"mitochondrial cyclophilin",
"CypD",
"CYP3"
]
}
],
"uuid": "a1a6d47b-4def-4ae8-ad7e-6f091db7590c"
}