{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0744DITV/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0744DITV",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-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": "missing publication",
"detail": "Measurement set [IGVFDS0744DITV](/measurement-sets/IGVFDS0744DITV/) 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/IGVFDS0744DITV/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS0744DITV](/measurement-sets/IGVFDS0744DITV/) has sequence file(s) [IGVFFI1073ZSLH](/sequence-files/IGVFFI1073ZSLH/), [IGVFFI2073IQFY](/sequence-files/IGVFFI2073IQFY/), [IGVFFI9425QVXR](/sequence-files/IGVFFI9425QVXR/), [IGVFFI2132TIXB](/sequence-files/IGVFFI2132TIXB/), [IGVFFI5421RNOS](/sequence-files/IGVFFI5421RNOS/), [IGVFFI8964OBGH](/sequence-files/IGVFFI8964OBGH/), [IGVFFI7685STPO](/sequence-files/IGVFFI7685STPO/), [IGVFFI3200EYFR](/sequence-files/IGVFFI3200EYFR/), [IGVFFI0194FZAD](/sequence-files/IGVFFI0194FZAD/), [IGVFFI2504QRRC](/sequence-files/IGVFFI2504QRRC/), [IGVFFI9727RMNQ](/sequence-files/IGVFFI9727RMNQ/), [IGVFFI4063OSHO](/sequence-files/IGVFFI4063OSHO/), [IGVFFI1471BZKW](/sequence-files/IGVFFI1471BZKW/), [IGVFFI9210NPAI](/sequence-files/IGVFFI9210NPAI/), [IGVFFI4297SGFU](/sequence-files/IGVFFI4297SGFU/), [IGVFFI0481IKPP](/sequence-files/IGVFFI0481IKPP/), [IGVFFI1007LTEP](/sequence-files/IGVFFI1007LTEP/), [IGVFFI3142XCZJ](/sequence-files/IGVFFI3142XCZJ/), [IGVFFI3918QBBM](/sequence-files/IGVFFI3918QBBM/), [IGVFFI8706DBCO](/sequence-files/IGVFFI8706DBCO/), [IGVFFI5642VKXS](/sequence-files/IGVFFI5642VKXS/), [IGVFFI1479STKN](/sequence-files/IGVFFI1479STKN/), [IGVFFI4689TRNY](/sequence-files/IGVFFI4689TRNY/), [IGVFFI8191KQII](/sequence-files/IGVFFI8191KQII/), [IGVFFI9496ZQBS](/sequence-files/IGVFFI9496ZQBS/), [IGVFFI1018EVZI](/sequence-files/IGVFFI1018EVZI/), [IGVFFI4964CBCT](/sequence-files/IGVFFI4964CBCT/), [IGVFFI4886QLWI](/sequence-files/IGVFFI4886QLWI/), [IGVFFI7326BLMW](/sequence-files/IGVFFI7326BLMW/), [IGVFFI2791LYTA](/sequence-files/IGVFFI2791LYTA/), [IGVFFI7832NMCV](/sequence-files/IGVFFI7832NMCV/), [IGVFFI4332KSVL](/sequence-files/IGVFFI4332KSVL/), [IGVFFI8584ONBJ](/sequence-files/IGVFFI8584ONBJ/), [IGVFFI2577KSQG](/sequence-files/IGVFFI2577KSQG/), [IGVFFI3136MTFR](/sequence-files/IGVFFI3136MTFR/), [IGVFFI8133SCWY](/sequence-files/IGVFFI8133SCWY/), [IGVFFI2721CXVA](/sequence-files/IGVFFI2721CXVA/), [IGVFFI5575EGRW](/sequence-files/IGVFFI5575EGRW/), [IGVFFI5796CPXD](/sequence-files/IGVFFI5796CPXD/), [IGVFFI3028EYTI](/sequence-files/IGVFFI3028EYTI/), [IGVFFI6687MPQG](/sequence-files/IGVFFI6687MPQG/), [IGVFFI1796QDGJ](/sequence-files/IGVFFI1796QDGJ/), [IGVFFI2796NLDA](/sequence-files/IGVFFI2796NLDA/), [IGVFFI5036QMNI](/sequence-files/IGVFFI5036QMNI/), [IGVFFI2621HAXU](/sequence-files/IGVFFI2621HAXU/), [IGVFFI7078JLCE](/sequence-files/IGVFFI7078JLCE/), [IGVFFI3324QJXL](/sequence-files/IGVFFI3324QJXL/), [IGVFFI0886WXJY](/sequence-files/IGVFFI0886WXJY/) 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/IGVFDS0744DITV/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS0744DITV](/measurement-sets/IGVFDS0744DITV/) has sequence file(s): [IGVFFI1073ZSLH](/sequence-files/IGVFFI1073ZSLH/), [IGVFFI2073IQFY](/sequence-files/IGVFFI2073IQFY/), [IGVFFI9425QVXR](/sequence-files/IGVFFI9425QVXR/), [IGVFFI2132TIXB](/sequence-files/IGVFFI2132TIXB/), [IGVFFI5421RNOS](/sequence-files/IGVFFI5421RNOS/), [IGVFFI8964OBGH](/sequence-files/IGVFFI8964OBGH/), [IGVFFI7685STPO](/sequence-files/IGVFFI7685STPO/), [IGVFFI3200EYFR](/sequence-files/IGVFFI3200EYFR/), [IGVFFI0194FZAD](/sequence-files/IGVFFI0194FZAD/), [IGVFFI2504QRRC](/sequence-files/IGVFFI2504QRRC/), [IGVFFI9727RMNQ](/sequence-files/IGVFFI9727RMNQ/), [IGVFFI4063OSHO](/sequence-files/IGVFFI4063OSHO/), [IGVFFI1471BZKW](/sequence-files/IGVFFI1471BZKW/), [IGVFFI9210NPAI](/sequence-files/IGVFFI9210NPAI/), [IGVFFI4297SGFU](/sequence-files/IGVFFI4297SGFU/), [IGVFFI0481IKPP](/sequence-files/IGVFFI0481IKPP/), [IGVFFI1007LTEP](/sequence-files/IGVFFI1007LTEP/), [IGVFFI3142XCZJ](/sequence-files/IGVFFI3142XCZJ/), [IGVFFI3918QBBM](/sequence-files/IGVFFI3918QBBM/), [IGVFFI8706DBCO](/sequence-files/IGVFFI8706DBCO/), [IGVFFI5642VKXS](/sequence-files/IGVFFI5642VKXS/), [IGVFFI1479STKN](/sequence-files/IGVFFI1479STKN/), [IGVFFI4689TRNY](/sequence-files/IGVFFI4689TRNY/), [IGVFFI8191KQII](/sequence-files/IGVFFI8191KQII/), [IGVFFI9496ZQBS](/sequence-files/IGVFFI9496ZQBS/), [IGVFFI1018EVZI](/sequence-files/IGVFFI1018EVZI/), [IGVFFI4964CBCT](/sequence-files/IGVFFI4964CBCT/), [IGVFFI4886QLWI](/sequence-files/IGVFFI4886QLWI/), [IGVFFI7326BLMW](/sequence-files/IGVFFI7326BLMW/), [IGVFFI2791LYTA](/sequence-files/IGVFFI2791LYTA/), [IGVFFI7832NMCV](/sequence-files/IGVFFI7832NMCV/), [IGVFFI4332KSVL](/sequence-files/IGVFFI4332KSVL/), [IGVFFI8584ONBJ](/sequence-files/IGVFFI8584ONBJ/), [IGVFFI2577KSQG](/sequence-files/IGVFFI2577KSQG/), [IGVFFI3136MTFR](/sequence-files/IGVFFI3136MTFR/), [IGVFFI8133SCWY](/sequence-files/IGVFFI8133SCWY/), [IGVFFI2721CXVA](/sequence-files/IGVFFI2721CXVA/), [IGVFFI5575EGRW](/sequence-files/IGVFFI5575EGRW/), [IGVFFI5796CPXD](/sequence-files/IGVFFI5796CPXD/), [IGVFFI3028EYTI](/sequence-files/IGVFFI3028EYTI/), [IGVFFI6687MPQG](/sequence-files/IGVFFI6687MPQG/), [IGVFFI1796QDGJ](/sequence-files/IGVFFI1796QDGJ/), [IGVFFI2796NLDA](/sequence-files/IGVFFI2796NLDA/), [IGVFFI5036QMNI](/sequence-files/IGVFFI5036QMNI/), [IGVFFI2621HAXU](/sequence-files/IGVFFI2621HAXU/), [IGVFFI7078JLCE](/sequence-files/IGVFFI7078JLCE/), [IGVFFI3324QJXL](/sequence-files/IGVFFI3324QJXL/), [IGVFFI0886WXJY](/sequence-files/IGVFFI0886WXJY/) 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/IGVFDS0744DITV/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM4599PEWQ](/in-vitro-systems/IGVFSM4599PEWQ/) 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/IGVFSM4599PEWQ/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM4599PEWQ](/in-vitro-systems/IGVFSM4599PEWQ/) 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/IGVFSM4599PEWQ/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS0744DITV](/measurement-sets/IGVFDS0744DITV/) 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/IGVFDS0744DITV/"
}
]
},
"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": "2023-11-30T22:50:08.154338+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/IGVFFI1073ZSLH/",
"accession": "IGVFFI1073ZSLH",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinA-PCRrep11_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:59:11.222534+00:00",
"file_format": "fastq",
"file_size": 4837839,
"href": "/sequence-files/IGVFFI1073ZSLH/@@download/IGVFFI1073ZSLH.fastq.gz",
"md5sum": "f03ea0ae9996dbf84cf97fcbded34273",
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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-BioRep2-FFrep4-BinA-PCRrep11_S347_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2073IQFY/",
"accession": "IGVFFI2073IQFY",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinA-PCRrep8_I1"
],
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"controlled_access": false,
"creation_timestamp": "2023-12-05T23:03:33.240802+00:00",
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"href": "/sequence-files/IGVFFI2073IQFY/@@download/IGVFFI2073IQFY.fastq.gz",
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9425QVXR/",
"accession": "IGVFFI9425QVXR",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinA-PCRrep5_I1"
],
"content_type": "reads",
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},
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"upload_status": "validated"
},
{
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"accession": "IGVFFI2132TIXB",
"aliases": [
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],
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},
"status": "released",
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"upload_status": "validated"
},
{
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"accession": "IGVFFI5421RNOS",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:04:25.823334+00:00",
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"sequencing_platform": {
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"status": "released",
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},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8964OBGH/",
"accession": "IGVFFI8964OBGH",
"aliases": [
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],
"content_type": "reads",
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},
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},
{
"@id": "/sequence-files/IGVFFI7685STPO/",
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],
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},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3200EYFR/",
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"aliases": [
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],
"content_type": "reads",
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0194FZAD/",
"accession": "IGVFFI0194FZAD",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
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},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2504QRRC/",
"accession": "IGVFFI2504QRRC",
"aliases": [
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],
"content_type": "reads",
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"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinA-PCRrep12_S348_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0886WXJY/",
"accession": "IGVFFI0886WXJY",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinA-PCRrep12_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:59:28.776409+00:00",
"file_format": "fastq",
"file_size": 1288540,
"href": "/sequence-files/IGVFFI0886WXJY/@@download/IGVFFI0886WXJY.fastq.gz",
"md5sum": "d506524adb0663f85f02064cce47c5fe",
"s3_uri": "s3://igvf-files/2023/12/05/2c800229-74a3-4d08-973e-eee8ebbad682/IGVFFI0886WXJY.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-BioRep2-FFrep4-BinA-PCRrep12_S348_I1_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": "2023-12-20T23:06:26.337442+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4599PEWQ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4599PEWQ",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-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": "2023-12-05T22:57:43.967463+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": "a5b47e31-7e20-43e5-9664-ba4c7d387bb8"
}