{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3226EEYN/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3226EEYN",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep3-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 [IGVFSM1276SAGC](/in-vitro-systems/IGVFSM1276SAGC/) 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/IGVFSM1276SAGC/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM1276SAGC](/in-vitro-systems/IGVFSM1276SAGC/) 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/IGVFSM1276SAGC/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS3226EEYN](/measurement-sets/IGVFDS3226EEYN/) 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/IGVFDS3226EEYN/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS3226EEYN](/measurement-sets/IGVFDS3226EEYN/) has sequence file(s) [IGVFFI9227SRQG](/sequence-files/IGVFFI9227SRQG/), [IGVFFI8635DCDS](/sequence-files/IGVFFI8635DCDS/), [IGVFFI1682NDCW](/sequence-files/IGVFFI1682NDCW/), [IGVFFI1568GETW](/sequence-files/IGVFFI1568GETW/), [IGVFFI0930OWAT](/sequence-files/IGVFFI0930OWAT/), [IGVFFI4733DDYX](/sequence-files/IGVFFI4733DDYX/), [IGVFFI0134RFFN](/sequence-files/IGVFFI0134RFFN/), [IGVFFI8086IBDD](/sequence-files/IGVFFI8086IBDD/), [IGVFFI1625KPDG](/sequence-files/IGVFFI1625KPDG/), [IGVFFI3024EVGP](/sequence-files/IGVFFI3024EVGP/), [IGVFFI2862QDNP](/sequence-files/IGVFFI2862QDNP/), [IGVFFI5535YYAZ](/sequence-files/IGVFFI5535YYAZ/), [IGVFFI0431VFNT](/sequence-files/IGVFFI0431VFNT/), [IGVFFI9816MGJM](/sequence-files/IGVFFI9816MGJM/), [IGVFFI7969QSXA](/sequence-files/IGVFFI7969QSXA/), [IGVFFI0697CAND](/sequence-files/IGVFFI0697CAND/), [IGVFFI0875GYEZ](/sequence-files/IGVFFI0875GYEZ/), [IGVFFI8086QEUR](/sequence-files/IGVFFI8086QEUR/), [IGVFFI3928JAJD](/sequence-files/IGVFFI3928JAJD/), [IGVFFI5335CVZT](/sequence-files/IGVFFI5335CVZT/), [IGVFFI0546YCUY](/sequence-files/IGVFFI0546YCUY/), [IGVFFI7550NQVG](/sequence-files/IGVFFI7550NQVG/), [IGVFFI4595SYCI](/sequence-files/IGVFFI4595SYCI/), [IGVFFI5622BSAS](/sequence-files/IGVFFI5622BSAS/), [IGVFFI6445ASHR](/sequence-files/IGVFFI6445ASHR/), [IGVFFI3407KLVJ](/sequence-files/IGVFFI3407KLVJ/), [IGVFFI2722AIYC](/sequence-files/IGVFFI2722AIYC/), [IGVFFI4965TODK](/sequence-files/IGVFFI4965TODK/), [IGVFFI5521UIZA](/sequence-files/IGVFFI5521UIZA/), [IGVFFI7271WIVU](/sequence-files/IGVFFI7271WIVU/), [IGVFFI6289UNNG](/sequence-files/IGVFFI6289UNNG/), [IGVFFI5344HGJX](/sequence-files/IGVFFI5344HGJX/), [IGVFFI9185UOPG](/sequence-files/IGVFFI9185UOPG/), [IGVFFI3813AYUH](/sequence-files/IGVFFI3813AYUH/), [IGVFFI8451XSWN](/sequence-files/IGVFFI8451XSWN/), [IGVFFI9301NLCR](/sequence-files/IGVFFI9301NLCR/), [IGVFFI0734CVAR](/sequence-files/IGVFFI0734CVAR/), [IGVFFI7663VGRF](/sequence-files/IGVFFI7663VGRF/), [IGVFFI0377DUPL](/sequence-files/IGVFFI0377DUPL/), [IGVFFI5775AHWO](/sequence-files/IGVFFI5775AHWO/), [IGVFFI3685PSAC](/sequence-files/IGVFFI3685PSAC/), [IGVFFI7914OJPO](/sequence-files/IGVFFI7914OJPO/), [IGVFFI5515SHCB](/sequence-files/IGVFFI5515SHCB/), [IGVFFI6685DMKS](/sequence-files/IGVFFI6685DMKS/), [IGVFFI9095RRES](/sequence-files/IGVFFI9095RRES/), [IGVFFI7461LBZI](/sequence-files/IGVFFI7461LBZI/), [IGVFFI3878WQYI](/sequence-files/IGVFFI3878WQYI/), [IGVFFI0121DDIA](/sequence-files/IGVFFI0121DDIA/) 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/IGVFDS3226EEYN/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS3226EEYN](/measurement-sets/IGVFDS3226EEYN/) has sequence file(s): [IGVFFI9227SRQG](/sequence-files/IGVFFI9227SRQG/), [IGVFFI8635DCDS](/sequence-files/IGVFFI8635DCDS/), [IGVFFI1682NDCW](/sequence-files/IGVFFI1682NDCW/), [IGVFFI1568GETW](/sequence-files/IGVFFI1568GETW/), [IGVFFI0930OWAT](/sequence-files/IGVFFI0930OWAT/), [IGVFFI4733DDYX](/sequence-files/IGVFFI4733DDYX/), [IGVFFI0134RFFN](/sequence-files/IGVFFI0134RFFN/), [IGVFFI8086IBDD](/sequence-files/IGVFFI8086IBDD/), [IGVFFI1625KPDG](/sequence-files/IGVFFI1625KPDG/), [IGVFFI3024EVGP](/sequence-files/IGVFFI3024EVGP/), [IGVFFI2862QDNP](/sequence-files/IGVFFI2862QDNP/), [IGVFFI5535YYAZ](/sequence-files/IGVFFI5535YYAZ/), [IGVFFI0431VFNT](/sequence-files/IGVFFI0431VFNT/), [IGVFFI9816MGJM](/sequence-files/IGVFFI9816MGJM/), [IGVFFI7969QSXA](/sequence-files/IGVFFI7969QSXA/), [IGVFFI0697CAND](/sequence-files/IGVFFI0697CAND/), [IGVFFI0875GYEZ](/sequence-files/IGVFFI0875GYEZ/), [IGVFFI8086QEUR](/sequence-files/IGVFFI8086QEUR/), [IGVFFI3928JAJD](/sequence-files/IGVFFI3928JAJD/), [IGVFFI5335CVZT](/sequence-files/IGVFFI5335CVZT/), [IGVFFI0546YCUY](/sequence-files/IGVFFI0546YCUY/), [IGVFFI7550NQVG](/sequence-files/IGVFFI7550NQVG/), [IGVFFI4595SYCI](/sequence-files/IGVFFI4595SYCI/), [IGVFFI5622BSAS](/sequence-files/IGVFFI5622BSAS/), [IGVFFI6445ASHR](/sequence-files/IGVFFI6445ASHR/), [IGVFFI3407KLVJ](/sequence-files/IGVFFI3407KLVJ/), [IGVFFI2722AIYC](/sequence-files/IGVFFI2722AIYC/), [IGVFFI4965TODK](/sequence-files/IGVFFI4965TODK/), [IGVFFI5521UIZA](/sequence-files/IGVFFI5521UIZA/), [IGVFFI7271WIVU](/sequence-files/IGVFFI7271WIVU/), [IGVFFI6289UNNG](/sequence-files/IGVFFI6289UNNG/), [IGVFFI5344HGJX](/sequence-files/IGVFFI5344HGJX/), [IGVFFI9185UOPG](/sequence-files/IGVFFI9185UOPG/), [IGVFFI3813AYUH](/sequence-files/IGVFFI3813AYUH/), [IGVFFI8451XSWN](/sequence-files/IGVFFI8451XSWN/), [IGVFFI9301NLCR](/sequence-files/IGVFFI9301NLCR/), [IGVFFI0734CVAR](/sequence-files/IGVFFI0734CVAR/), [IGVFFI7663VGRF](/sequence-files/IGVFFI7663VGRF/), [IGVFFI0377DUPL](/sequence-files/IGVFFI0377DUPL/), [IGVFFI5775AHWO](/sequence-files/IGVFFI5775AHWO/), [IGVFFI3685PSAC](/sequence-files/IGVFFI3685PSAC/), [IGVFFI7914OJPO](/sequence-files/IGVFFI7914OJPO/), [IGVFFI5515SHCB](/sequence-files/IGVFFI5515SHCB/), [IGVFFI6685DMKS](/sequence-files/IGVFFI6685DMKS/), [IGVFFI9095RRES](/sequence-files/IGVFFI9095RRES/), [IGVFFI7461LBZI](/sequence-files/IGVFFI7461LBZI/), [IGVFFI3878WQYI](/sequence-files/IGVFFI3878WQYI/), [IGVFFI0121DDIA](/sequence-files/IGVFFI0121DDIA/) 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/IGVFDS3226EEYN/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS3226EEYN](/measurement-sets/IGVFDS3226EEYN/) 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/IGVFDS3226EEYN/"
}
]
},
"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": "2023-11-30T22:49:45.713286+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/IGVFFI9227SRQG/",
"accession": "IGVFFI9227SRQG",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep3-BinD-PCRrep10_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:53:36.188598+00:00",
"file_format": "fastq",
"file_size": 1842264,
"href": "/sequence-files/IGVFFI9227SRQG/@@download/IGVFFI9227SRQG.fastq.gz",
"md5sum": "d77c7321ed74fdd9c9f8d8c814914b32",
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"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep3-BinD-PCRrep10_S142_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8635DCDS/",
"accession": "IGVFFI8635DCDS",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep3-BinD-PCRrep7_R1"
],
"content_type": "reads",
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"creation_timestamp": "2023-12-05T20:59:05.274593+00:00",
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"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep3-BinD-PCRrep7_S139_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1682NDCW/",
"accession": "IGVFFI1682NDCW",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep3-BinD-PCRrep8_I1"
],
"content_type": "reads",
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1568GETW/",
"accession": "IGVFFI1568GETW",
"aliases": [
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],
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},
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},
{
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"accession": "IGVFFI0930OWAT",
"aliases": [
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],
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4733DDYX/",
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"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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],
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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/IGVFFI1625KPDG/",
"accession": "IGVFFI1625KPDG",
"aliases": [
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],
"content_type": "reads",
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},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3024EVGP/",
"accession": "IGVFFI3024EVGP",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:58:35.274892+00:00",
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"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep3-BinD-PCRrep12_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:55:03.772192+00:00",
"file_format": "fastq",
"file_size": 5218568,
"href": "/sequence-files/IGVFFI0121DDIA/@@download/IGVFFI0121DDIA.fastq.gz",
"md5sum": "4a350e3042a600a9d9c2aef38586f025",
"s3_uri": "s3://igvf-files/2023/12/05/28bab400-5d43-4aab-a9d5-9db4914c04a9/IGVFFI0121DDIA.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-FFrep3-BinD-PCRrep12_S144_R1_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": "2023-12-20T23:06:03.099075+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1276SAGC/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1276SAGC",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep3-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": "2023-12-05T20:53:01.123406+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": "7c89c6c1-e288-42ac-a0e4-f5b6c8777f1c"
}