{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8854UNCC/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8854UNCC",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-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": "mismatched status",
"detail": "Released in vitro system [IGVFSM0996COAP](/in-vitro-systems/IGVFSM0996COAP/) has in progress subobject construct library set [IGVFDS6982DESN](/construct-library-sets/IGVFDS6982DESN/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM0996COAP/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM0996COAP](/in-vitro-systems/IGVFSM0996COAP/) 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/IGVFSM0996COAP/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS8854UNCC](/measurement-sets/IGVFDS8854UNCC/) 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/IGVFDS8854UNCC/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS8854UNCC](/measurement-sets/IGVFDS8854UNCC/) has sequence file(s) [IGVFFI4711CIXX](/sequence-files/IGVFFI4711CIXX/), [IGVFFI6689KHJP](/sequence-files/IGVFFI6689KHJP/), [IGVFFI2229WOYS](/sequence-files/IGVFFI2229WOYS/), [IGVFFI9102FSTO](/sequence-files/IGVFFI9102FSTO/), [IGVFFI5938AHQA](/sequence-files/IGVFFI5938AHQA/), [IGVFFI9469DOMZ](/sequence-files/IGVFFI9469DOMZ/), [IGVFFI2308VGTZ](/sequence-files/IGVFFI2308VGTZ/), [IGVFFI1017VHCR](/sequence-files/IGVFFI1017VHCR/), [IGVFFI8781NAKB](/sequence-files/IGVFFI8781NAKB/), [IGVFFI7700MJJC](/sequence-files/IGVFFI7700MJJC/), [IGVFFI2110LCBU](/sequence-files/IGVFFI2110LCBU/), [IGVFFI5946TCXD](/sequence-files/IGVFFI5946TCXD/), [IGVFFI5996IRJR](/sequence-files/IGVFFI5996IRJR/), [IGVFFI8881PRJY](/sequence-files/IGVFFI8881PRJY/), [IGVFFI7482OATK](/sequence-files/IGVFFI7482OATK/), [IGVFFI9592EUOO](/sequence-files/IGVFFI9592EUOO/), [IGVFFI6894KDSY](/sequence-files/IGVFFI6894KDSY/), [IGVFFI4809NEBF](/sequence-files/IGVFFI4809NEBF/), [IGVFFI0444UZDT](/sequence-files/IGVFFI0444UZDT/), [IGVFFI2533OGLW](/sequence-files/IGVFFI2533OGLW/), [IGVFFI2263YDDY](/sequence-files/IGVFFI2263YDDY/), [IGVFFI0953DPVO](/sequence-files/IGVFFI0953DPVO/), [IGVFFI0805HWKK](/sequence-files/IGVFFI0805HWKK/), [IGVFFI1435ISXK](/sequence-files/IGVFFI1435ISXK/), [IGVFFI1508FAVA](/sequence-files/IGVFFI1508FAVA/), [IGVFFI2317QZGK](/sequence-files/IGVFFI2317QZGK/), [IGVFFI7086ASGT](/sequence-files/IGVFFI7086ASGT/), [IGVFFI0524NRVI](/sequence-files/IGVFFI0524NRVI/), [IGVFFI9113MZCT](/sequence-files/IGVFFI9113MZCT/), [IGVFFI6660EPGZ](/sequence-files/IGVFFI6660EPGZ/), [IGVFFI7572DLBQ](/sequence-files/IGVFFI7572DLBQ/), [IGVFFI3368ENLL](/sequence-files/IGVFFI3368ENLL/), [IGVFFI1161UNCP](/sequence-files/IGVFFI1161UNCP/), [IGVFFI2614FBKI](/sequence-files/IGVFFI2614FBKI/), [IGVFFI4007TUZS](/sequence-files/IGVFFI4007TUZS/), [IGVFFI4228VCEE](/sequence-files/IGVFFI4228VCEE/), [IGVFFI5885LRJY](/sequence-files/IGVFFI5885LRJY/), [IGVFFI7761YETU](/sequence-files/IGVFFI7761YETU/), [IGVFFI4975VEMN](/sequence-files/IGVFFI4975VEMN/), [IGVFFI8440EVIN](/sequence-files/IGVFFI8440EVIN/), [IGVFFI6926DFZL](/sequence-files/IGVFFI6926DFZL/), [IGVFFI1904ZVLM](/sequence-files/IGVFFI1904ZVLM/), [IGVFFI4475YJDD](/sequence-files/IGVFFI4475YJDD/), [IGVFFI3725DANG](/sequence-files/IGVFFI3725DANG/), [IGVFFI4801EXVQ](/sequence-files/IGVFFI4801EXVQ/), [IGVFFI6849FWGH](/sequence-files/IGVFFI6849FWGH/), [IGVFFI0408SGWQ](/sequence-files/IGVFFI0408SGWQ/), [IGVFFI8481DQGI](/sequence-files/IGVFFI8481DQGI/) 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/IGVFDS8854UNCC/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS8854UNCC](/measurement-sets/IGVFDS8854UNCC/) has sequence file(s): [IGVFFI4711CIXX](/sequence-files/IGVFFI4711CIXX/), [IGVFFI6689KHJP](/sequence-files/IGVFFI6689KHJP/), [IGVFFI2229WOYS](/sequence-files/IGVFFI2229WOYS/), [IGVFFI9102FSTO](/sequence-files/IGVFFI9102FSTO/), [IGVFFI5938AHQA](/sequence-files/IGVFFI5938AHQA/), [IGVFFI9469DOMZ](/sequence-files/IGVFFI9469DOMZ/), [IGVFFI2308VGTZ](/sequence-files/IGVFFI2308VGTZ/), [IGVFFI1017VHCR](/sequence-files/IGVFFI1017VHCR/), [IGVFFI8781NAKB](/sequence-files/IGVFFI8781NAKB/), [IGVFFI7700MJJC](/sequence-files/IGVFFI7700MJJC/), [IGVFFI2110LCBU](/sequence-files/IGVFFI2110LCBU/), [IGVFFI5946TCXD](/sequence-files/IGVFFI5946TCXD/), [IGVFFI5996IRJR](/sequence-files/IGVFFI5996IRJR/), [IGVFFI8881PRJY](/sequence-files/IGVFFI8881PRJY/), [IGVFFI7482OATK](/sequence-files/IGVFFI7482OATK/), [IGVFFI9592EUOO](/sequence-files/IGVFFI9592EUOO/), [IGVFFI6894KDSY](/sequence-files/IGVFFI6894KDSY/), [IGVFFI4809NEBF](/sequence-files/IGVFFI4809NEBF/), [IGVFFI0444UZDT](/sequence-files/IGVFFI0444UZDT/), [IGVFFI2533OGLW](/sequence-files/IGVFFI2533OGLW/), [IGVFFI2263YDDY](/sequence-files/IGVFFI2263YDDY/), [IGVFFI0953DPVO](/sequence-files/IGVFFI0953DPVO/), [IGVFFI0805HWKK](/sequence-files/IGVFFI0805HWKK/), [IGVFFI1435ISXK](/sequence-files/IGVFFI1435ISXK/), [IGVFFI1508FAVA](/sequence-files/IGVFFI1508FAVA/), [IGVFFI2317QZGK](/sequence-files/IGVFFI2317QZGK/), [IGVFFI7086ASGT](/sequence-files/IGVFFI7086ASGT/), [IGVFFI0524NRVI](/sequence-files/IGVFFI0524NRVI/), [IGVFFI9113MZCT](/sequence-files/IGVFFI9113MZCT/), [IGVFFI6660EPGZ](/sequence-files/IGVFFI6660EPGZ/), [IGVFFI7572DLBQ](/sequence-files/IGVFFI7572DLBQ/), [IGVFFI3368ENLL](/sequence-files/IGVFFI3368ENLL/), [IGVFFI1161UNCP](/sequence-files/IGVFFI1161UNCP/), [IGVFFI2614FBKI](/sequence-files/IGVFFI2614FBKI/), [IGVFFI4007TUZS](/sequence-files/IGVFFI4007TUZS/), [IGVFFI4228VCEE](/sequence-files/IGVFFI4228VCEE/), [IGVFFI5885LRJY](/sequence-files/IGVFFI5885LRJY/), [IGVFFI7761YETU](/sequence-files/IGVFFI7761YETU/), [IGVFFI4975VEMN](/sequence-files/IGVFFI4975VEMN/), [IGVFFI8440EVIN](/sequence-files/IGVFFI8440EVIN/), [IGVFFI6926DFZL](/sequence-files/IGVFFI6926DFZL/), [IGVFFI1904ZVLM](/sequence-files/IGVFFI1904ZVLM/), [IGVFFI4475YJDD](/sequence-files/IGVFFI4475YJDD/), [IGVFFI3725DANG](/sequence-files/IGVFFI3725DANG/), [IGVFFI4801EXVQ](/sequence-files/IGVFFI4801EXVQ/), [IGVFFI6849FWGH](/sequence-files/IGVFFI6849FWGH/), [IGVFFI0408SGWQ](/sequence-files/IGVFFI0408SGWQ/), [IGVFFI8481DQGI](/sequence-files/IGVFFI8481DQGI/) 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/IGVFDS8854UNCC/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS8854UNCC](/measurement-sets/IGVFDS8854UNCC/) 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/IGVFDS8854UNCC/"
}
]
},
"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/IGVFDS6982DESN/",
"accession": "IGVFDS6982DESN",
"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/IGVFDS5864UGFT/",
"accession": "IGVFDS5864UGFT",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-THP1-PE2_Exp2_NegControl_AmpliconSequencing"
],
"status": "released"
}
],
"control_for": [],
"creation_timestamp": "2023-11-30T22:49:50.951097+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": "IGVFFI4711CIXX",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinD-PCRrep10_R1"
],
"content_type": "reads",
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"creation_timestamp": "2023-12-05T21:24:51.243321+00:00",
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"md5sum": "75cc146dc30e069d784841f0ccc9e6a6",
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"sequencing_platform": {
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"term_name": "Illumina NextSeq 550"
},
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"upload_status": "validated"
},
{
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"accession": "IGVFFI6689KHJP",
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],
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},
"status": "released",
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"upload_status": "validated"
},
{
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"accession": "IGVFFI2229WOYS",
"aliases": [
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],
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"upload_status": "validated"
},
{
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"aliases": [
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},
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},
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"aliases": [
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},
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},
{
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"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/IGVFFI2308VGTZ/",
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"aliases": [
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],
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},
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"aliases": [
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],
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},
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"upload_status": "validated"
},
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"aliases": [
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],
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"controlled_access": false,
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},
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"upload_status": "validated"
},
{
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"aliases": [
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],
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"controlled_access": false,
"creation_timestamp": "2023-12-05T21:28:21.656402+00:00",
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"@id": "/sequence-files/IGVFFI8481DQGI/",
"accession": "IGVFFI8481DQGI",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinD-PCRrep8_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:30:14.685317+00:00",
"file_format": "fastq",
"file_size": 7487294,
"href": "/sequence-files/IGVFFI8481DQGI/@@download/IGVFFI8481DQGI.fastq.gz",
"md5sum": "4fedd197a5529ebc8da1506c71494b4e",
"s3_uri": "s3://igvf-files/2023/12/05/345d79bb-6206-49e8-982f-c10c8c7bdb80/IGVFFI8481DQGI.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinD-PCRrep8_S188_R2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS3423PSID/"
],
"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": "2023-12-20T23:06:48.483415+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0996COAP/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0996COAP",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-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": "2023-12-05T21:23:58.559617+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": "977878ca-40eb-4d59-b146-98fc9806fcbc"
}