{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9915OTKB/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9915OTKB",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep3-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": "mismatched status",
"detail": "Released in vitro system [IGVFSM4653AWMR](/in-vitro-systems/IGVFSM4653AWMR/) 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/IGVFSM4653AWMR/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM4653AWMR](/in-vitro-systems/IGVFSM4653AWMR/) 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/IGVFSM4653AWMR/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS9915OTKB](/measurement-sets/IGVFDS9915OTKB/) 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/IGVFDS9915OTKB/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS9915OTKB](/measurement-sets/IGVFDS9915OTKB/) has sequence file(s) [IGVFFI8999AFEL](/sequence-files/IGVFFI8999AFEL/), [IGVFFI6137DAJM](/sequence-files/IGVFFI6137DAJM/), [IGVFFI8078JNPC](/sequence-files/IGVFFI8078JNPC/), [IGVFFI2375HWTM](/sequence-files/IGVFFI2375HWTM/), [IGVFFI2098HSWE](/sequence-files/IGVFFI2098HSWE/), [IGVFFI7502ZASD](/sequence-files/IGVFFI7502ZASD/), [IGVFFI8836HDDL](/sequence-files/IGVFFI8836HDDL/), [IGVFFI3970TSLH](/sequence-files/IGVFFI3970TSLH/), [IGVFFI2905GGAF](/sequence-files/IGVFFI2905GGAF/), [IGVFFI8507SFLB](/sequence-files/IGVFFI8507SFLB/), [IGVFFI3936XXTY](/sequence-files/IGVFFI3936XXTY/), [IGVFFI1295AUWL](/sequence-files/IGVFFI1295AUWL/), [IGVFFI0015ASLT](/sequence-files/IGVFFI0015ASLT/), [IGVFFI5571ZPJC](/sequence-files/IGVFFI5571ZPJC/), [IGVFFI1484WZPG](/sequence-files/IGVFFI1484WZPG/), [IGVFFI6122RYGE](/sequence-files/IGVFFI6122RYGE/), [IGVFFI7836URTT](/sequence-files/IGVFFI7836URTT/), [IGVFFI2676JDMJ](/sequence-files/IGVFFI2676JDMJ/), [IGVFFI2163RSHW](/sequence-files/IGVFFI2163RSHW/), [IGVFFI4077PIWE](/sequence-files/IGVFFI4077PIWE/), [IGVFFI4084EQMC](/sequence-files/IGVFFI4084EQMC/), [IGVFFI9446EEEU](/sequence-files/IGVFFI9446EEEU/), [IGVFFI7012PAOC](/sequence-files/IGVFFI7012PAOC/), [IGVFFI6174JVIL](/sequence-files/IGVFFI6174JVIL/), [IGVFFI7497HPLY](/sequence-files/IGVFFI7497HPLY/), [IGVFFI5504DRIE](/sequence-files/IGVFFI5504DRIE/), [IGVFFI3323VCYB](/sequence-files/IGVFFI3323VCYB/), [IGVFFI0895UIJG](/sequence-files/IGVFFI0895UIJG/), [IGVFFI5106PKFS](/sequence-files/IGVFFI5106PKFS/), [IGVFFI5357BCXC](/sequence-files/IGVFFI5357BCXC/), [IGVFFI7664KCTF](/sequence-files/IGVFFI7664KCTF/), [IGVFFI0943PFGG](/sequence-files/IGVFFI0943PFGG/), [IGVFFI7919IXKG](/sequence-files/IGVFFI7919IXKG/), [IGVFFI3871RPTV](/sequence-files/IGVFFI3871RPTV/), [IGVFFI0228KHUN](/sequence-files/IGVFFI0228KHUN/), [IGVFFI6659CIEL](/sequence-files/IGVFFI6659CIEL/), [IGVFFI3735SBMG](/sequence-files/IGVFFI3735SBMG/), [IGVFFI1055IHQX](/sequence-files/IGVFFI1055IHQX/), [IGVFFI1360AWJA](/sequence-files/IGVFFI1360AWJA/), [IGVFFI1167GINQ](/sequence-files/IGVFFI1167GINQ/), [IGVFFI8811XLSG](/sequence-files/IGVFFI8811XLSG/), [IGVFFI5777HFXF](/sequence-files/IGVFFI5777HFXF/), [IGVFFI0798GSWP](/sequence-files/IGVFFI0798GSWP/), [IGVFFI8392OFNI](/sequence-files/IGVFFI8392OFNI/), [IGVFFI1586MSVN](/sequence-files/IGVFFI1586MSVN/), [IGVFFI9263ZQYP](/sequence-files/IGVFFI9263ZQYP/), [IGVFFI1499UKUL](/sequence-files/IGVFFI1499UKUL/), [IGVFFI8110DIWC](/sequence-files/IGVFFI8110DIWC/) 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/IGVFDS9915OTKB/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS9915OTKB](/measurement-sets/IGVFDS9915OTKB/) has sequence file(s): [IGVFFI8999AFEL](/sequence-files/IGVFFI8999AFEL/), [IGVFFI6137DAJM](/sequence-files/IGVFFI6137DAJM/), [IGVFFI8078JNPC](/sequence-files/IGVFFI8078JNPC/), [IGVFFI2375HWTM](/sequence-files/IGVFFI2375HWTM/), [IGVFFI2098HSWE](/sequence-files/IGVFFI2098HSWE/), [IGVFFI7502ZASD](/sequence-files/IGVFFI7502ZASD/), [IGVFFI8836HDDL](/sequence-files/IGVFFI8836HDDL/), [IGVFFI3970TSLH](/sequence-files/IGVFFI3970TSLH/), [IGVFFI2905GGAF](/sequence-files/IGVFFI2905GGAF/), [IGVFFI8507SFLB](/sequence-files/IGVFFI8507SFLB/), [IGVFFI3936XXTY](/sequence-files/IGVFFI3936XXTY/), [IGVFFI1295AUWL](/sequence-files/IGVFFI1295AUWL/), [IGVFFI0015ASLT](/sequence-files/IGVFFI0015ASLT/), [IGVFFI5571ZPJC](/sequence-files/IGVFFI5571ZPJC/), [IGVFFI1484WZPG](/sequence-files/IGVFFI1484WZPG/), [IGVFFI6122RYGE](/sequence-files/IGVFFI6122RYGE/), [IGVFFI7836URTT](/sequence-files/IGVFFI7836URTT/), [IGVFFI2676JDMJ](/sequence-files/IGVFFI2676JDMJ/), [IGVFFI2163RSHW](/sequence-files/IGVFFI2163RSHW/), [IGVFFI4077PIWE](/sequence-files/IGVFFI4077PIWE/), [IGVFFI4084EQMC](/sequence-files/IGVFFI4084EQMC/), [IGVFFI9446EEEU](/sequence-files/IGVFFI9446EEEU/), [IGVFFI7012PAOC](/sequence-files/IGVFFI7012PAOC/), [IGVFFI6174JVIL](/sequence-files/IGVFFI6174JVIL/), [IGVFFI7497HPLY](/sequence-files/IGVFFI7497HPLY/), [IGVFFI5504DRIE](/sequence-files/IGVFFI5504DRIE/), [IGVFFI3323VCYB](/sequence-files/IGVFFI3323VCYB/), [IGVFFI0895UIJG](/sequence-files/IGVFFI0895UIJG/), [IGVFFI5106PKFS](/sequence-files/IGVFFI5106PKFS/), [IGVFFI5357BCXC](/sequence-files/IGVFFI5357BCXC/), [IGVFFI7664KCTF](/sequence-files/IGVFFI7664KCTF/), [IGVFFI0943PFGG](/sequence-files/IGVFFI0943PFGG/), [IGVFFI7919IXKG](/sequence-files/IGVFFI7919IXKG/), [IGVFFI3871RPTV](/sequence-files/IGVFFI3871RPTV/), [IGVFFI0228KHUN](/sequence-files/IGVFFI0228KHUN/), [IGVFFI6659CIEL](/sequence-files/IGVFFI6659CIEL/), [IGVFFI3735SBMG](/sequence-files/IGVFFI3735SBMG/), [IGVFFI1055IHQX](/sequence-files/IGVFFI1055IHQX/), [IGVFFI1360AWJA](/sequence-files/IGVFFI1360AWJA/), [IGVFFI1167GINQ](/sequence-files/IGVFFI1167GINQ/), [IGVFFI8811XLSG](/sequence-files/IGVFFI8811XLSG/), [IGVFFI5777HFXF](/sequence-files/IGVFFI5777HFXF/), [IGVFFI0798GSWP](/sequence-files/IGVFFI0798GSWP/), [IGVFFI8392OFNI](/sequence-files/IGVFFI8392OFNI/), [IGVFFI1586MSVN](/sequence-files/IGVFFI1586MSVN/), [IGVFFI9263ZQYP](/sequence-files/IGVFFI9263ZQYP/), [IGVFFI1499UKUL](/sequence-files/IGVFFI1499UKUL/), [IGVFFI8110DIWC](/sequence-files/IGVFFI8110DIWC/) 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/IGVFDS9915OTKB/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS9915OTKB](/measurement-sets/IGVFDS9915OTKB/) 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/IGVFDS9915OTKB/"
}
]
},
"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": "2023-11-30T22:49:18.541788+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": [
{
"@id": "/sequence-files/IGVFFI8999AFEL/",
"accession": "IGVFFI8999AFEL",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep3-BinA-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:54:51.225343+00:00",
"file_format": "fastq",
"file_size": 855639,
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"md5sum": "9b0765ead8e97ff9e4ac4d6e8b33764c",
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"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep3-BinA-PCRrep2_S200_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6137DAJM/",
"accession": "IGVFFI6137DAJM",
"aliases": [
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],
"content_type": "reads",
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},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8078JNPC/",
"accession": "IGVFFI8078JNPC",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep3-BinA-PCRrep5_R2"
],
"content_type": "reads",
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},
"status": "released",
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},
{
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"accession": "IGVFFI2375HWTM",
"aliases": [
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],
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},
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"upload_status": "validated"
},
{
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"accession": "IGVFFI2098HSWE",
"aliases": [
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],
"content_type": "reads",
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},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7502ZASD/",
"accession": "IGVFFI7502ZASD",
"aliases": [
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],
"content_type": "reads",
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8836HDDL/",
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"aliases": [
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],
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},
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},
{
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"accession": "IGVFFI3970TSLH",
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],
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2905GGAF/",
"accession": "IGVFFI2905GGAF",
"aliases": [
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],
"content_type": "reads",
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8507SFLB/",
"accession": "IGVFFI8507SFLB",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep3-BinA-PCRrep7_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:58:16.142857+00:00",
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"s3_uri": "s3://igvf-files/2023/12/05/b43abc58-baa4-4e3f-b31f-70071d1feb58/IGVFFI1499UKUL.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-BioRep2-FFrep3-BinA-PCRrep8_S296_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8110DIWC/",
"accession": "IGVFFI8110DIWC",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep3-BinA-PCRrep6_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:57:39.152121+00:00",
"file_format": "fastq",
"file_size": 3638325,
"href": "/sequence-files/IGVFFI8110DIWC/@@download/IGVFFI8110DIWC.fastq.gz",
"md5sum": "117882928fe938c93b8735b49155dbef",
"s3_uri": "s3://igvf-files/2023/12/05/c6eba0fe-08bb-4df4-a521-614e3a405499/IGVFFI8110DIWC.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-BioRep2-FFrep3-BinA-PCRrep6_S204_R2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS5031MNRR/"
],
"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": "2023-12-20T23:05:45.479636+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4653AWMR/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4653AWMR",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep3-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_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 0-25% 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": "2023-12-05T22:52:12.966981+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": "0b3cdd6d-a4e0-4bfa-bdc6-3efd3a2a2a6f"
}