{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8825HZQT/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8825HZQT",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-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": "mismatched status",
"detail": "Released in vitro system [IGVFSM4715APXQ](/in-vitro-systems/IGVFSM4715APXQ/) 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/IGVFSM4715APXQ/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM4715APXQ](/in-vitro-systems/IGVFSM4715APXQ/) 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/IGVFSM4715APXQ/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS8825HZQT](/measurement-sets/IGVFDS8825HZQT/) 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/IGVFDS8825HZQT/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS8825HZQT](/measurement-sets/IGVFDS8825HZQT/) has sequence file(s) [IGVFFI8457MWDA](/sequence-files/IGVFFI8457MWDA/), [IGVFFI6109UNCR](/sequence-files/IGVFFI6109UNCR/), [IGVFFI4019BGWH](/sequence-files/IGVFFI4019BGWH/), [IGVFFI0064LGEU](/sequence-files/IGVFFI0064LGEU/), [IGVFFI2739AIFP](/sequence-files/IGVFFI2739AIFP/), [IGVFFI4721ITCQ](/sequence-files/IGVFFI4721ITCQ/), [IGVFFI7636KOYI](/sequence-files/IGVFFI7636KOYI/), [IGVFFI0896LPWU](/sequence-files/IGVFFI0896LPWU/), [IGVFFI4672VVGA](/sequence-files/IGVFFI4672VVGA/), [IGVFFI6861PCSM](/sequence-files/IGVFFI6861PCSM/), [IGVFFI8688VRMK](/sequence-files/IGVFFI8688VRMK/), [IGVFFI0012TTRW](/sequence-files/IGVFFI0012TTRW/), [IGVFFI4964MKCU](/sequence-files/IGVFFI4964MKCU/), [IGVFFI4815WHQF](/sequence-files/IGVFFI4815WHQF/), [IGVFFI6135MUAN](/sequence-files/IGVFFI6135MUAN/), [IGVFFI2857IQLP](/sequence-files/IGVFFI2857IQLP/), [IGVFFI1357XWPE](/sequence-files/IGVFFI1357XWPE/), [IGVFFI6417SRHN](/sequence-files/IGVFFI6417SRHN/), [IGVFFI4013OTUX](/sequence-files/IGVFFI4013OTUX/), [IGVFFI4659XZHC](/sequence-files/IGVFFI4659XZHC/), [IGVFFI5032UAVV](/sequence-files/IGVFFI5032UAVV/), [IGVFFI7009XXKU](/sequence-files/IGVFFI7009XXKU/), [IGVFFI6786YWMW](/sequence-files/IGVFFI6786YWMW/), [IGVFFI5140PUDK](/sequence-files/IGVFFI5140PUDK/), [IGVFFI3933MHTF](/sequence-files/IGVFFI3933MHTF/), [IGVFFI6769YIOO](/sequence-files/IGVFFI6769YIOO/), [IGVFFI9468HPTU](/sequence-files/IGVFFI9468HPTU/), [IGVFFI9041MRBG](/sequence-files/IGVFFI9041MRBG/), [IGVFFI0160QFYO](/sequence-files/IGVFFI0160QFYO/), [IGVFFI5118SZNZ](/sequence-files/IGVFFI5118SZNZ/), [IGVFFI8399COXZ](/sequence-files/IGVFFI8399COXZ/), [IGVFFI6230GMMZ](/sequence-files/IGVFFI6230GMMZ/), [IGVFFI4292OYFZ](/sequence-files/IGVFFI4292OYFZ/), [IGVFFI9375NUNV](/sequence-files/IGVFFI9375NUNV/), [IGVFFI3973SKSO](/sequence-files/IGVFFI3973SKSO/), [IGVFFI6849QXIH](/sequence-files/IGVFFI6849QXIH/), [IGVFFI7198MWCQ](/sequence-files/IGVFFI7198MWCQ/), [IGVFFI9627UZBY](/sequence-files/IGVFFI9627UZBY/), [IGVFFI2950NCXE](/sequence-files/IGVFFI2950NCXE/), [IGVFFI4883FVQH](/sequence-files/IGVFFI4883FVQH/), [IGVFFI5160NBFB](/sequence-files/IGVFFI5160NBFB/), [IGVFFI8590QQRL](/sequence-files/IGVFFI8590QQRL/), [IGVFFI9624YHWV](/sequence-files/IGVFFI9624YHWV/), [IGVFFI9887RYJC](/sequence-files/IGVFFI9887RYJC/), [IGVFFI1457IGQN](/sequence-files/IGVFFI1457IGQN/), [IGVFFI1859OWLZ](/sequence-files/IGVFFI1859OWLZ/), [IGVFFI4671UMMP](/sequence-files/IGVFFI4671UMMP/), [IGVFFI9912IKZS](/sequence-files/IGVFFI9912IKZS/) 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/IGVFDS8825HZQT/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS8825HZQT](/measurement-sets/IGVFDS8825HZQT/) has sequence file(s): [IGVFFI8457MWDA](/sequence-files/IGVFFI8457MWDA/), [IGVFFI6109UNCR](/sequence-files/IGVFFI6109UNCR/), [IGVFFI4019BGWH](/sequence-files/IGVFFI4019BGWH/), [IGVFFI0064LGEU](/sequence-files/IGVFFI0064LGEU/), [IGVFFI2739AIFP](/sequence-files/IGVFFI2739AIFP/), [IGVFFI4721ITCQ](/sequence-files/IGVFFI4721ITCQ/), [IGVFFI7636KOYI](/sequence-files/IGVFFI7636KOYI/), [IGVFFI0896LPWU](/sequence-files/IGVFFI0896LPWU/), [IGVFFI4672VVGA](/sequence-files/IGVFFI4672VVGA/), [IGVFFI6861PCSM](/sequence-files/IGVFFI6861PCSM/), [IGVFFI8688VRMK](/sequence-files/IGVFFI8688VRMK/), [IGVFFI0012TTRW](/sequence-files/IGVFFI0012TTRW/), [IGVFFI4964MKCU](/sequence-files/IGVFFI4964MKCU/), [IGVFFI4815WHQF](/sequence-files/IGVFFI4815WHQF/), [IGVFFI6135MUAN](/sequence-files/IGVFFI6135MUAN/), [IGVFFI2857IQLP](/sequence-files/IGVFFI2857IQLP/), [IGVFFI1357XWPE](/sequence-files/IGVFFI1357XWPE/), [IGVFFI6417SRHN](/sequence-files/IGVFFI6417SRHN/), [IGVFFI4013OTUX](/sequence-files/IGVFFI4013OTUX/), [IGVFFI4659XZHC](/sequence-files/IGVFFI4659XZHC/), [IGVFFI5032UAVV](/sequence-files/IGVFFI5032UAVV/), [IGVFFI7009XXKU](/sequence-files/IGVFFI7009XXKU/), [IGVFFI6786YWMW](/sequence-files/IGVFFI6786YWMW/), [IGVFFI5140PUDK](/sequence-files/IGVFFI5140PUDK/), [IGVFFI3933MHTF](/sequence-files/IGVFFI3933MHTF/), [IGVFFI6769YIOO](/sequence-files/IGVFFI6769YIOO/), [IGVFFI9468HPTU](/sequence-files/IGVFFI9468HPTU/), [IGVFFI9041MRBG](/sequence-files/IGVFFI9041MRBG/), [IGVFFI0160QFYO](/sequence-files/IGVFFI0160QFYO/), [IGVFFI5118SZNZ](/sequence-files/IGVFFI5118SZNZ/), [IGVFFI8399COXZ](/sequence-files/IGVFFI8399COXZ/), [IGVFFI6230GMMZ](/sequence-files/IGVFFI6230GMMZ/), [IGVFFI4292OYFZ](/sequence-files/IGVFFI4292OYFZ/), [IGVFFI9375NUNV](/sequence-files/IGVFFI9375NUNV/), [IGVFFI3973SKSO](/sequence-files/IGVFFI3973SKSO/), [IGVFFI6849QXIH](/sequence-files/IGVFFI6849QXIH/), [IGVFFI7198MWCQ](/sequence-files/IGVFFI7198MWCQ/), [IGVFFI9627UZBY](/sequence-files/IGVFFI9627UZBY/), [IGVFFI2950NCXE](/sequence-files/IGVFFI2950NCXE/), [IGVFFI4883FVQH](/sequence-files/IGVFFI4883FVQH/), [IGVFFI5160NBFB](/sequence-files/IGVFFI5160NBFB/), [IGVFFI8590QQRL](/sequence-files/IGVFFI8590QQRL/), [IGVFFI9624YHWV](/sequence-files/IGVFFI9624YHWV/), [IGVFFI9887RYJC](/sequence-files/IGVFFI9887RYJC/), [IGVFFI1457IGQN](/sequence-files/IGVFFI1457IGQN/), [IGVFFI1859OWLZ](/sequence-files/IGVFFI1859OWLZ/), [IGVFFI4671UMMP](/sequence-files/IGVFFI4671UMMP/), [IGVFFI9912IKZS](/sequence-files/IGVFFI9912IKZS/) 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/IGVFDS8825HZQT/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS8825HZQT](/measurement-sets/IGVFDS8825HZQT/) 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/IGVFDS8825HZQT/"
}
]
},
"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": "2023-11-30T22:49:27.820796+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/IGVFFI8457MWDA/",
"accession": "IGVFFI8457MWDA",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-BinC-PCRrep6_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:44:17.583394+00:00",
"file_format": "fastq",
"file_size": 788179,
"href": "/sequence-files/IGVFFI8457MWDA/@@download/IGVFFI8457MWDA.fastq.gz",
"md5sum": "1921d8163b1c514dd93bcfafba21c2f9",
"s3_uri": "s3://igvf-files/2023/12/05/5da6c4c5-60d8-41ca-ba1e-f0bf23be025d/IGVFFI8457MWDA.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-BioRep2-FFrep4-BinC-PCRrep6_S276_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6109UNCR/",
"accession": "IGVFFI6109UNCR",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-BinC-PCRrep8_I1"
],
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4019BGWH/",
"accession": "IGVFFI4019BGWH",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-BinC-PCRrep9_R2"
],
"content_type": "reads",
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},
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"upload_status": "validated"
},
{
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"accession": "IGVFFI0064LGEU",
"aliases": [
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],
"content_type": "reads",
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},
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},
{
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"aliases": [
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"content_type": "reads",
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},
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},
{
"@id": "/sequence-files/IGVFFI4721ITCQ/",
"accession": "IGVFFI4721ITCQ",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7636KOYI/",
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"aliases": [
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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/IGVFFI4672VVGA/",
"accession": "IGVFFI4672VVGA",
"aliases": [
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],
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6861PCSM/",
"accession": "IGVFFI6861PCSM",
"aliases": [
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],
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"href": "/sequence-files/IGVFFI4671UMMP/@@download/IGVFFI4671UMMP.fastq.gz",
"md5sum": "1ea0e74923ec43ec7909d77f2f046da9",
"s3_uri": "s3://igvf-files/2023/12/05/9b75c175-8c68-4b8d-9d94-f73be8e6d218/IGVFFI4671UMMP.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-BioRep2-FFrep4-BinC-PCRrep3_S273_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9912IKZS/",
"accession": "IGVFFI9912IKZS",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-BinC-PCRrep12_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:41:19.423164+00:00",
"file_format": "fastq",
"file_size": 870596,
"href": "/sequence-files/IGVFFI9912IKZS/@@download/IGVFFI9912IKZS.fastq.gz",
"md5sum": "12b1db3c1a84c2e70df1812c2c986e91",
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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-FFrep4-BinC-PCRrep12_S372_I2_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": "2023-12-20T23:05:26.229156+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4715APXQ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4715APXQ",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-BinC"
],
"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 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": "2023-12-05T23:39:18.287867+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": "2db029f6-7008-4f7e-abf1-a5745b96660c"
}