{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1183IGHQ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1183IGHQ",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep2-BinC_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 publication",
"detail": "Measurement set [IGVFDS1183IGHQ](/measurement-sets/IGVFDS1183IGHQ/) 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/IGVFDS1183IGHQ/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS1183IGHQ](/measurement-sets/IGVFDS1183IGHQ/) has sequence file(s) [IGVFFI3728ZQEQ](/sequence-files/IGVFFI3728ZQEQ/), [IGVFFI9826RBMH](/sequence-files/IGVFFI9826RBMH/), [IGVFFI5847NKOA](/sequence-files/IGVFFI5847NKOA/), [IGVFFI5651JALQ](/sequence-files/IGVFFI5651JALQ/), [IGVFFI8084FSEC](/sequence-files/IGVFFI8084FSEC/), [IGVFFI6462ESFJ](/sequence-files/IGVFFI6462ESFJ/), [IGVFFI2465ILOV](/sequence-files/IGVFFI2465ILOV/), [IGVFFI6744TABI](/sequence-files/IGVFFI6744TABI/), [IGVFFI8025MMQZ](/sequence-files/IGVFFI8025MMQZ/), [IGVFFI8543PVDX](/sequence-files/IGVFFI8543PVDX/), [IGVFFI8137SRKK](/sequence-files/IGVFFI8137SRKK/), [IGVFFI0141BQZM](/sequence-files/IGVFFI0141BQZM/), [IGVFFI3343MTND](/sequence-files/IGVFFI3343MTND/), [IGVFFI8836ZHYP](/sequence-files/IGVFFI8836ZHYP/), [IGVFFI7987LULC](/sequence-files/IGVFFI7987LULC/), [IGVFFI0149RJDR](/sequence-files/IGVFFI0149RJDR/), [IGVFFI2657QGHY](/sequence-files/IGVFFI2657QGHY/), [IGVFFI9820WVVB](/sequence-files/IGVFFI9820WVVB/), [IGVFFI2468ZLFL](/sequence-files/IGVFFI2468ZLFL/), [IGVFFI1509CDJI](/sequence-files/IGVFFI1509CDJI/), [IGVFFI0762MMIS](/sequence-files/IGVFFI0762MMIS/), [IGVFFI3419PXKY](/sequence-files/IGVFFI3419PXKY/), [IGVFFI3314GITF](/sequence-files/IGVFFI3314GITF/), [IGVFFI5833QCSW](/sequence-files/IGVFFI5833QCSW/), [IGVFFI1698XFQK](/sequence-files/IGVFFI1698XFQK/), [IGVFFI5074HBNB](/sequence-files/IGVFFI5074HBNB/), [IGVFFI6125FUFL](/sequence-files/IGVFFI6125FUFL/), [IGVFFI6676DZDL](/sequence-files/IGVFFI6676DZDL/), [IGVFFI5006GIAG](/sequence-files/IGVFFI5006GIAG/), [IGVFFI2764FWSY](/sequence-files/IGVFFI2764FWSY/), [IGVFFI1518PSCH](/sequence-files/IGVFFI1518PSCH/), [IGVFFI4108GXYS](/sequence-files/IGVFFI4108GXYS/), [IGVFFI7796MJQE](/sequence-files/IGVFFI7796MJQE/), [IGVFFI6154QZFM](/sequence-files/IGVFFI6154QZFM/), [IGVFFI4504VICY](/sequence-files/IGVFFI4504VICY/), [IGVFFI6493GTRD](/sequence-files/IGVFFI6493GTRD/), [IGVFFI5654MYJJ](/sequence-files/IGVFFI5654MYJJ/), [IGVFFI9153AWHD](/sequence-files/IGVFFI9153AWHD/), [IGVFFI1895LRMV](/sequence-files/IGVFFI1895LRMV/), [IGVFFI3706XGBG](/sequence-files/IGVFFI3706XGBG/), [IGVFFI6223MGNU](/sequence-files/IGVFFI6223MGNU/), [IGVFFI7988IXWV](/sequence-files/IGVFFI7988IXWV/), [IGVFFI6152YZDN](/sequence-files/IGVFFI6152YZDN/), [IGVFFI9832POMT](/sequence-files/IGVFFI9832POMT/), [IGVFFI8291ZSJI](/sequence-files/IGVFFI8291ZSJI/), [IGVFFI2974OLAJ](/sequence-files/IGVFFI2974OLAJ/), [IGVFFI1637QHDU](/sequence-files/IGVFFI1637QHDU/), [IGVFFI9439GRGN](/sequence-files/IGVFFI9439GRGN/) 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/IGVFDS1183IGHQ/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS1183IGHQ](/measurement-sets/IGVFDS1183IGHQ/) has sequence file(s): [IGVFFI3728ZQEQ](/sequence-files/IGVFFI3728ZQEQ/), [IGVFFI9826RBMH](/sequence-files/IGVFFI9826RBMH/), [IGVFFI5847NKOA](/sequence-files/IGVFFI5847NKOA/), [IGVFFI5651JALQ](/sequence-files/IGVFFI5651JALQ/), [IGVFFI8084FSEC](/sequence-files/IGVFFI8084FSEC/), [IGVFFI6462ESFJ](/sequence-files/IGVFFI6462ESFJ/), [IGVFFI2465ILOV](/sequence-files/IGVFFI2465ILOV/), [IGVFFI6744TABI](/sequence-files/IGVFFI6744TABI/), [IGVFFI8025MMQZ](/sequence-files/IGVFFI8025MMQZ/), [IGVFFI8543PVDX](/sequence-files/IGVFFI8543PVDX/), [IGVFFI8137SRKK](/sequence-files/IGVFFI8137SRKK/), [IGVFFI0141BQZM](/sequence-files/IGVFFI0141BQZM/), [IGVFFI3343MTND](/sequence-files/IGVFFI3343MTND/), [IGVFFI8836ZHYP](/sequence-files/IGVFFI8836ZHYP/), [IGVFFI7987LULC](/sequence-files/IGVFFI7987LULC/), [IGVFFI0149RJDR](/sequence-files/IGVFFI0149RJDR/), [IGVFFI2657QGHY](/sequence-files/IGVFFI2657QGHY/), [IGVFFI9820WVVB](/sequence-files/IGVFFI9820WVVB/), [IGVFFI2468ZLFL](/sequence-files/IGVFFI2468ZLFL/), [IGVFFI1509CDJI](/sequence-files/IGVFFI1509CDJI/), [IGVFFI0762MMIS](/sequence-files/IGVFFI0762MMIS/), [IGVFFI3419PXKY](/sequence-files/IGVFFI3419PXKY/), [IGVFFI3314GITF](/sequence-files/IGVFFI3314GITF/), [IGVFFI5833QCSW](/sequence-files/IGVFFI5833QCSW/), [IGVFFI1698XFQK](/sequence-files/IGVFFI1698XFQK/), [IGVFFI5074HBNB](/sequence-files/IGVFFI5074HBNB/), [IGVFFI6125FUFL](/sequence-files/IGVFFI6125FUFL/), [IGVFFI6676DZDL](/sequence-files/IGVFFI6676DZDL/), [IGVFFI5006GIAG](/sequence-files/IGVFFI5006GIAG/), [IGVFFI2764FWSY](/sequence-files/IGVFFI2764FWSY/), [IGVFFI1518PSCH](/sequence-files/IGVFFI1518PSCH/), [IGVFFI4108GXYS](/sequence-files/IGVFFI4108GXYS/), [IGVFFI7796MJQE](/sequence-files/IGVFFI7796MJQE/), [IGVFFI6154QZFM](/sequence-files/IGVFFI6154QZFM/), [IGVFFI4504VICY](/sequence-files/IGVFFI4504VICY/), [IGVFFI6493GTRD](/sequence-files/IGVFFI6493GTRD/), [IGVFFI5654MYJJ](/sequence-files/IGVFFI5654MYJJ/), [IGVFFI9153AWHD](/sequence-files/IGVFFI9153AWHD/), [IGVFFI1895LRMV](/sequence-files/IGVFFI1895LRMV/), [IGVFFI3706XGBG](/sequence-files/IGVFFI3706XGBG/), [IGVFFI6223MGNU](/sequence-files/IGVFFI6223MGNU/), [IGVFFI7988IXWV](/sequence-files/IGVFFI7988IXWV/), [IGVFFI6152YZDN](/sequence-files/IGVFFI6152YZDN/), [IGVFFI9832POMT](/sequence-files/IGVFFI9832POMT/), [IGVFFI8291ZSJI](/sequence-files/IGVFFI8291ZSJI/), [IGVFFI2974OLAJ](/sequence-files/IGVFFI2974OLAJ/), [IGVFFI1637QHDU](/sequence-files/IGVFFI1637QHDU/), [IGVFFI9439GRGN](/sequence-files/IGVFFI9439GRGN/) 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/IGVFDS1183IGHQ/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM3771MMDC](/in-vitro-systems/IGVFSM3771MMDC/) has in progress subobject construct library set [IGVFDS2374NXLW](/construct-library-sets/IGVFDS2374NXLW/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM3771MMDC/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM3771MMDC](/in-vitro-systems/IGVFSM3771MMDC/) 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/IGVFSM3771MMDC/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS1183IGHQ](/measurement-sets/IGVFDS1183IGHQ/) 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/IGVFDS1183IGHQ/"
}
]
},
"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/IGVFDS2374NXLW/",
"accession": "IGVFDS2374NXLW",
"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/IGVFDS4989HPTW/",
"accession": "IGVFDS4989HPTW",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-THP1-PE2_Exp1_NegControl_AmpliconSequencing"
],
"status": "released"
}
],
"control_for": [],
"creation_timestamp": "2023-11-30T22:48:55.791991+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"accession": "IGVFDO7359LVPI",
"aliases": [
"igvf:donor_of_THP1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI3728ZQEQ/",
"accession": "IGVFFI3728ZQEQ",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep2-BinC-PCRrep5_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:03:56.692775+00:00",
"file_format": "fastq",
"file_size": 3405705,
"href": "/sequence-files/IGVFFI3728ZQEQ/@@download/IGVFFI3728ZQEQ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/cc93e794-e684-4e0f-9b93-0dce77eda8e3/IGVFFI3728ZQEQ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep2-BinC-PCRrep5_S77_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9826RBMH/",
"accession": "IGVFFI9826RBMH",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep2-BinC-PCRrep7_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:05:20.430128+00:00",
"file_format": "fastq",
"file_size": 6994959,
"href": "/sequence-files/IGVFFI9826RBMH/@@download/IGVFFI9826RBMH.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/45a9b3f9-9338-4e95-9772-4c612179906f/IGVFFI9826RBMH.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep2-BinC-PCRrep7_S169_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5847NKOA/",
"accession": "IGVFFI5847NKOA",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep2-BinC-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:02:00.028605+00:00",
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"href": "/sequence-files/IGVFFI5847NKOA/@@download/IGVFFI5847NKOA.fastq.gz",
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5651JALQ/",
"accession": "IGVFFI5651JALQ",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep2-BinC-PCRrep3_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:02:46.851403+00:00",
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"file_size": 3997259,
"href": "/sequence-files/IGVFFI5651JALQ/@@download/IGVFFI5651JALQ.fastq.gz",
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8084FSEC/",
"accession": "IGVFFI8084FSEC",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:00:31.786025+00:00",
"file_format": "fastq",
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"href": "/sequence-files/IGVFFI8084FSEC/@@download/IGVFFI8084FSEC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/5e96e1a0-82e8-4391-be23-d43b5e96e476/IGVFFI8084FSEC.fastq.gz",
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep2-BinC-PCRrep11_S173_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6462ESFJ/",
"accession": "IGVFFI6462ESFJ",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep2-BinC-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:01:37.921212+00:00",
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"file_size": 958094,
"href": "/sequence-files/IGVFFI6462ESFJ/@@download/IGVFFI6462ESFJ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/a1c547f9-beb8-4a39-8f00-2484ffc37566/IGVFFI6462ESFJ.fastq.gz",
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
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},
{
"@id": "/sequence-files/IGVFFI2465ILOV/",
"accession": "IGVFFI2465ILOV",
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],
"content_type": "reads",
"controlled_access": false,
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"term_name": "Illumina NextSeq 550"
},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6744TABI/",
"accession": "IGVFFI6744TABI",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep2-BinC-PCRrep12_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:01:28.555864+00:00",
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"href": "/sequence-files/IGVFFI6744TABI/@@download/IGVFFI6744TABI.fastq.gz",
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8025MMQZ/",
"accession": "IGVFFI8025MMQZ",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:02:09.707497+00:00",
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},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8543PVDX/",
"accession": "IGVFFI8543PVDX",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep2-BinC-PCRrep11_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:00:50.169971+00:00",
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"status": "released",
"term_name": "Illumina NextSeq 550"
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"summary": "Homo sapiens (male) THP-1 cell line (sorting details: FACS bin for 51-75% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T19:59:07.764195+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": "5923baf9-7599-44ef-bf9d-373f1b5c4039"
}