{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5989CMGV/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5989CMGV",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep4-BinD_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 [IGVFDS5989CMGV](/measurement-sets/IGVFDS5989CMGV/) 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/IGVFDS5989CMGV/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS5989CMGV](/measurement-sets/IGVFDS5989CMGV/) has sequence file(s) [IGVFFI9521LRMI](/sequence-files/IGVFFI9521LRMI/), [IGVFFI5033XRYC](/sequence-files/IGVFFI5033XRYC/), [IGVFFI7126VQGS](/sequence-files/IGVFFI7126VQGS/), [IGVFFI0602YNVT](/sequence-files/IGVFFI0602YNVT/), [IGVFFI0941IHTC](/sequence-files/IGVFFI0941IHTC/), [IGVFFI0009GKYA](/sequence-files/IGVFFI0009GKYA/), [IGVFFI8498JKWN](/sequence-files/IGVFFI8498JKWN/), [IGVFFI2438CQCG](/sequence-files/IGVFFI2438CQCG/), [IGVFFI4361HBPI](/sequence-files/IGVFFI4361HBPI/), [IGVFFI0920QAYV](/sequence-files/IGVFFI0920QAYV/), [IGVFFI7536MNPC](/sequence-files/IGVFFI7536MNPC/), [IGVFFI8588CSBG](/sequence-files/IGVFFI8588CSBG/), [IGVFFI5482MGKP](/sequence-files/IGVFFI5482MGKP/), [IGVFFI3769XPUX](/sequence-files/IGVFFI3769XPUX/), [IGVFFI5121MVQG](/sequence-files/IGVFFI5121MVQG/), [IGVFFI6400ZQFH](/sequence-files/IGVFFI6400ZQFH/), [IGVFFI5681BOAH](/sequence-files/IGVFFI5681BOAH/), [IGVFFI2136ZJAA](/sequence-files/IGVFFI2136ZJAA/), [IGVFFI0104FJGC](/sequence-files/IGVFFI0104FJGC/), [IGVFFI8767PLYE](/sequence-files/IGVFFI8767PLYE/), [IGVFFI1343ZPNK](/sequence-files/IGVFFI1343ZPNK/), [IGVFFI1083LRXG](/sequence-files/IGVFFI1083LRXG/), [IGVFFI5977KBMH](/sequence-files/IGVFFI5977KBMH/), [IGVFFI6222JDKE](/sequence-files/IGVFFI6222JDKE/), [IGVFFI6997GSHI](/sequence-files/IGVFFI6997GSHI/), [IGVFFI3068ABNC](/sequence-files/IGVFFI3068ABNC/), [IGVFFI5896IWCP](/sequence-files/IGVFFI5896IWCP/), [IGVFFI9537UXCI](/sequence-files/IGVFFI9537UXCI/), [IGVFFI3017VZYI](/sequence-files/IGVFFI3017VZYI/), [IGVFFI9213OBXS](/sequence-files/IGVFFI9213OBXS/), [IGVFFI7906ALEA](/sequence-files/IGVFFI7906ALEA/), [IGVFFI5200VCMJ](/sequence-files/IGVFFI5200VCMJ/), [IGVFFI0324VHNX](/sequence-files/IGVFFI0324VHNX/), [IGVFFI7439WXME](/sequence-files/IGVFFI7439WXME/), [IGVFFI4874UENK](/sequence-files/IGVFFI4874UENK/), [IGVFFI9360YJEE](/sequence-files/IGVFFI9360YJEE/), [IGVFFI5041QXNG](/sequence-files/IGVFFI5041QXNG/), [IGVFFI8225HALF](/sequence-files/IGVFFI8225HALF/), [IGVFFI9485NQMY](/sequence-files/IGVFFI9485NQMY/), [IGVFFI8211BKIT](/sequence-files/IGVFFI8211BKIT/), [IGVFFI2379DRXI](/sequence-files/IGVFFI2379DRXI/), [IGVFFI0610XCUI](/sequence-files/IGVFFI0610XCUI/), [IGVFFI8946IQIS](/sequence-files/IGVFFI8946IQIS/), [IGVFFI0110TQIE](/sequence-files/IGVFFI0110TQIE/), [IGVFFI5751WILI](/sequence-files/IGVFFI5751WILI/), [IGVFFI3220EFZK](/sequence-files/IGVFFI3220EFZK/), [IGVFFI1309JQES](/sequence-files/IGVFFI1309JQES/), [IGVFFI9962POYP](/sequence-files/IGVFFI9962POYP/) 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/IGVFDS5989CMGV/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS5989CMGV](/measurement-sets/IGVFDS5989CMGV/) has sequence file(s): [IGVFFI9521LRMI](/sequence-files/IGVFFI9521LRMI/), [IGVFFI5033XRYC](/sequence-files/IGVFFI5033XRYC/), [IGVFFI7126VQGS](/sequence-files/IGVFFI7126VQGS/), [IGVFFI0602YNVT](/sequence-files/IGVFFI0602YNVT/), [IGVFFI0941IHTC](/sequence-files/IGVFFI0941IHTC/), [IGVFFI0009GKYA](/sequence-files/IGVFFI0009GKYA/), [IGVFFI8498JKWN](/sequence-files/IGVFFI8498JKWN/), [IGVFFI2438CQCG](/sequence-files/IGVFFI2438CQCG/), [IGVFFI4361HBPI](/sequence-files/IGVFFI4361HBPI/), [IGVFFI0920QAYV](/sequence-files/IGVFFI0920QAYV/), [IGVFFI7536MNPC](/sequence-files/IGVFFI7536MNPC/), [IGVFFI8588CSBG](/sequence-files/IGVFFI8588CSBG/), [IGVFFI5482MGKP](/sequence-files/IGVFFI5482MGKP/), [IGVFFI3769XPUX](/sequence-files/IGVFFI3769XPUX/), [IGVFFI5121MVQG](/sequence-files/IGVFFI5121MVQG/), [IGVFFI6400ZQFH](/sequence-files/IGVFFI6400ZQFH/), [IGVFFI5681BOAH](/sequence-files/IGVFFI5681BOAH/), [IGVFFI2136ZJAA](/sequence-files/IGVFFI2136ZJAA/), [IGVFFI0104FJGC](/sequence-files/IGVFFI0104FJGC/), [IGVFFI8767PLYE](/sequence-files/IGVFFI8767PLYE/), [IGVFFI1343ZPNK](/sequence-files/IGVFFI1343ZPNK/), [IGVFFI1083LRXG](/sequence-files/IGVFFI1083LRXG/), [IGVFFI5977KBMH](/sequence-files/IGVFFI5977KBMH/), [IGVFFI6222JDKE](/sequence-files/IGVFFI6222JDKE/), [IGVFFI6997GSHI](/sequence-files/IGVFFI6997GSHI/), [IGVFFI3068ABNC](/sequence-files/IGVFFI3068ABNC/), [IGVFFI5896IWCP](/sequence-files/IGVFFI5896IWCP/), [IGVFFI9537UXCI](/sequence-files/IGVFFI9537UXCI/), [IGVFFI3017VZYI](/sequence-files/IGVFFI3017VZYI/), [IGVFFI9213OBXS](/sequence-files/IGVFFI9213OBXS/), [IGVFFI7906ALEA](/sequence-files/IGVFFI7906ALEA/), [IGVFFI5200VCMJ](/sequence-files/IGVFFI5200VCMJ/), [IGVFFI0324VHNX](/sequence-files/IGVFFI0324VHNX/), [IGVFFI7439WXME](/sequence-files/IGVFFI7439WXME/), [IGVFFI4874UENK](/sequence-files/IGVFFI4874UENK/), [IGVFFI9360YJEE](/sequence-files/IGVFFI9360YJEE/), [IGVFFI5041QXNG](/sequence-files/IGVFFI5041QXNG/), [IGVFFI8225HALF](/sequence-files/IGVFFI8225HALF/), [IGVFFI9485NQMY](/sequence-files/IGVFFI9485NQMY/), [IGVFFI8211BKIT](/sequence-files/IGVFFI8211BKIT/), [IGVFFI2379DRXI](/sequence-files/IGVFFI2379DRXI/), [IGVFFI0610XCUI](/sequence-files/IGVFFI0610XCUI/), [IGVFFI8946IQIS](/sequence-files/IGVFFI8946IQIS/), [IGVFFI0110TQIE](/sequence-files/IGVFFI0110TQIE/), [IGVFFI5751WILI](/sequence-files/IGVFFI5751WILI/), [IGVFFI3220EFZK](/sequence-files/IGVFFI3220EFZK/), [IGVFFI1309JQES](/sequence-files/IGVFFI1309JQES/), [IGVFFI9962POYP](/sequence-files/IGVFFI9962POYP/) 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/IGVFDS5989CMGV/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM4690OPZT](/in-vitro-systems/IGVFSM4690OPZT/) has in progress subobject construct library set [IGVFDS2385DHZO](/construct-library-sets/IGVFDS2385DHZO/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM4690OPZT/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM4690OPZT](/in-vitro-systems/IGVFSM4690OPZT/) 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/IGVFSM4690OPZT/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS5989CMGV](/measurement-sets/IGVFDS5989CMGV/) 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/IGVFDS5989CMGV/"
}
]
},
"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/IGVFDS2385DHZO/",
"accession": "IGVFDS2385DHZO",
"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/IGVFDS5128CXIS/",
"accession": "IGVFDS5128CXIS",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-THP1-PE2_Exp4_NegControl_AmpliconSequencing"
],
"status": "released"
}
],
"control_for": [],
"creation_timestamp": "2023-12-13T08:01:42.678922+00:00",
"data_use_limitation_summaries": [
"no certificate"
],
"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": [
{
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"accession": "IGVFFI9521LRMI",
"aliases": [
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5033XRYC/",
"accession": "IGVFFI5033XRYC",
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],
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},
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},
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},
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},
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},
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},
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},
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0920QAYV/",
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"submitted_file_name": "230523pPPIFEnformerTHP1-THP1-PE-pPPIF_Enformer-Amp-pPPIF-BioRep1-FFRep4_BinD-PCRrep6_S186_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1309JQES/",
"accession": "IGVFFI1309JQES",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep4-BinD-PCRrep8_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T09:55:33.099456+00:00",
"file_format": "fastq",
"file_size": 17893415,
"href": "/sequence-files/IGVFFI1309JQES/@@download/IGVFFI1309JQES.fastq.gz",
"md5sum": "36206dc424653cd7d44c4973f6595c67",
"s3_uri": "s3://igvf-files/2023/12/13/84d51d90-55b3-44b3-9d2f-4d379ba67a93/IGVFFI1309JQES.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230523pPPIFEnformerTHP1-THP1-PE-pPPIF_Enformer-Amp-pPPIF-BioRep1-FFRep4_BinD-PCRrep8_S188_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9962POYP/",
"accession": "IGVFFI9962POYP",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep4-BinD-PCRrep8_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T15:29:28.609380+00:00",
"file_format": "fastq",
"file_size": 3097908,
"href": "/sequence-files/IGVFFI9962POYP/@@download/IGVFFI9962POYP.fastq.gz",
"md5sum": "130cfab56d3ab13125006deb0dbd4ed1",
"s3_uri": "s3://igvf-files/2023/12/13/0ed6f8c7-4145-4ec9-ab0f-533c6ac66d07/IGVFFI9962POYP.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230523pPPIFEnformerTHP1-THP1-PE-pPPIF_Enformer-Amp-pPPIF-BioRep1-FFRep4_BinD-PCRrep8_S188_I1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4359OODY/"
],
"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": "2023-12-20T23:07:25.215701+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4690OPZT/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4690OPZT",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep4-BinD"
],
"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_0001253/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:THP-1"
],
"status": "released",
"summary": "THP-1",
"term_name": "THP-1"
}
],
"status": "released",
"summary": "Homo sapiens (male) THP-1 cell line (sorting details: FACS bin for 76-100% 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": "2023-12-13T08:42:30.231090+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": "588703b9-4af8-4313-bd22-5f17c0cb3483"
}