{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6622DPIT/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6622DPIT",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep1-BinB_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 [IGVFSM0143XZGF](/in-vitro-systems/IGVFSM0143XZGF/) 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/IGVFSM0143XZGF/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM0143XZGF](/in-vitro-systems/IGVFSM0143XZGF/) 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/IGVFSM0143XZGF/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS6622DPIT](/measurement-sets/IGVFDS6622DPIT/) 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/IGVFDS6622DPIT/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS6622DPIT](/measurement-sets/IGVFDS6622DPIT/) has sequence file(s) [IGVFFI1614ULLM](/sequence-files/IGVFFI1614ULLM/), [IGVFFI0530QDVG](/sequence-files/IGVFFI0530QDVG/), [IGVFFI0204LBGG](/sequence-files/IGVFFI0204LBGG/), [IGVFFI2287DQPO](/sequence-files/IGVFFI2287DQPO/), [IGVFFI8909RVBH](/sequence-files/IGVFFI8909RVBH/), [IGVFFI5712YUFB](/sequence-files/IGVFFI5712YUFB/), [IGVFFI0713TGNB](/sequence-files/IGVFFI0713TGNB/), [IGVFFI4900YRTW](/sequence-files/IGVFFI4900YRTW/), [IGVFFI3827SBBP](/sequence-files/IGVFFI3827SBBP/), [IGVFFI2636QMFX](/sequence-files/IGVFFI2636QMFX/), [IGVFFI9641TFLF](/sequence-files/IGVFFI9641TFLF/), [IGVFFI5599YHLM](/sequence-files/IGVFFI5599YHLM/), [IGVFFI8630MITX](/sequence-files/IGVFFI8630MITX/), [IGVFFI6064GCNQ](/sequence-files/IGVFFI6064GCNQ/), [IGVFFI6981FKWV](/sequence-files/IGVFFI6981FKWV/), [IGVFFI8787GEIZ](/sequence-files/IGVFFI8787GEIZ/), [IGVFFI5402YLHJ](/sequence-files/IGVFFI5402YLHJ/), [IGVFFI4499NPAO](/sequence-files/IGVFFI4499NPAO/), [IGVFFI5401OERY](/sequence-files/IGVFFI5401OERY/), [IGVFFI7498DHHY](/sequence-files/IGVFFI7498DHHY/), [IGVFFI0324DUDM](/sequence-files/IGVFFI0324DUDM/), [IGVFFI8893HDMU](/sequence-files/IGVFFI8893HDMU/), [IGVFFI8320BMTO](/sequence-files/IGVFFI8320BMTO/), [IGVFFI3214HBSH](/sequence-files/IGVFFI3214HBSH/), [IGVFFI4977SRGI](/sequence-files/IGVFFI4977SRGI/), [IGVFFI7741KCBL](/sequence-files/IGVFFI7741KCBL/), [IGVFFI6792MVVQ](/sequence-files/IGVFFI6792MVVQ/), [IGVFFI7980BYFW](/sequence-files/IGVFFI7980BYFW/), [IGVFFI8821XNHL](/sequence-files/IGVFFI8821XNHL/), [IGVFFI2454KXWO](/sequence-files/IGVFFI2454KXWO/), [IGVFFI3560UZZB](/sequence-files/IGVFFI3560UZZB/), [IGVFFI6942JVNS](/sequence-files/IGVFFI6942JVNS/), [IGVFFI7479JTPN](/sequence-files/IGVFFI7479JTPN/), [IGVFFI9650HDVE](/sequence-files/IGVFFI9650HDVE/), [IGVFFI1608WOSR](/sequence-files/IGVFFI1608WOSR/), [IGVFFI9346RSQU](/sequence-files/IGVFFI9346RSQU/), [IGVFFI4480XZFW](/sequence-files/IGVFFI4480XZFW/), [IGVFFI4339JATS](/sequence-files/IGVFFI4339JATS/), [IGVFFI4436RISI](/sequence-files/IGVFFI4436RISI/), [IGVFFI5971MRUB](/sequence-files/IGVFFI5971MRUB/), [IGVFFI7418XODT](/sequence-files/IGVFFI7418XODT/), [IGVFFI6307ZZKZ](/sequence-files/IGVFFI6307ZZKZ/), [IGVFFI9356QVZH](/sequence-files/IGVFFI9356QVZH/), [IGVFFI5579SHRT](/sequence-files/IGVFFI5579SHRT/), [IGVFFI4311QEZM](/sequence-files/IGVFFI4311QEZM/), [IGVFFI7665FNBQ](/sequence-files/IGVFFI7665FNBQ/), [IGVFFI9726EBVJ](/sequence-files/IGVFFI9726EBVJ/), [IGVFFI9601YCMM](/sequence-files/IGVFFI9601YCMM/) 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/IGVFDS6622DPIT/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS6622DPIT](/measurement-sets/IGVFDS6622DPIT/) has sequence file(s): [IGVFFI1614ULLM](/sequence-files/IGVFFI1614ULLM/), [IGVFFI0530QDVG](/sequence-files/IGVFFI0530QDVG/), [IGVFFI0204LBGG](/sequence-files/IGVFFI0204LBGG/), [IGVFFI2287DQPO](/sequence-files/IGVFFI2287DQPO/), [IGVFFI8909RVBH](/sequence-files/IGVFFI8909RVBH/), [IGVFFI5712YUFB](/sequence-files/IGVFFI5712YUFB/), [IGVFFI0713TGNB](/sequence-files/IGVFFI0713TGNB/), [IGVFFI4900YRTW](/sequence-files/IGVFFI4900YRTW/), [IGVFFI3827SBBP](/sequence-files/IGVFFI3827SBBP/), [IGVFFI2636QMFX](/sequence-files/IGVFFI2636QMFX/), [IGVFFI9641TFLF](/sequence-files/IGVFFI9641TFLF/), [IGVFFI5599YHLM](/sequence-files/IGVFFI5599YHLM/), [IGVFFI8630MITX](/sequence-files/IGVFFI8630MITX/), [IGVFFI6064GCNQ](/sequence-files/IGVFFI6064GCNQ/), [IGVFFI6981FKWV](/sequence-files/IGVFFI6981FKWV/), [IGVFFI8787GEIZ](/sequence-files/IGVFFI8787GEIZ/), [IGVFFI5402YLHJ](/sequence-files/IGVFFI5402YLHJ/), [IGVFFI4499NPAO](/sequence-files/IGVFFI4499NPAO/), [IGVFFI5401OERY](/sequence-files/IGVFFI5401OERY/), [IGVFFI7498DHHY](/sequence-files/IGVFFI7498DHHY/), [IGVFFI0324DUDM](/sequence-files/IGVFFI0324DUDM/), [IGVFFI8893HDMU](/sequence-files/IGVFFI8893HDMU/), [IGVFFI8320BMTO](/sequence-files/IGVFFI8320BMTO/), [IGVFFI3214HBSH](/sequence-files/IGVFFI3214HBSH/), [IGVFFI4977SRGI](/sequence-files/IGVFFI4977SRGI/), [IGVFFI7741KCBL](/sequence-files/IGVFFI7741KCBL/), [IGVFFI6792MVVQ](/sequence-files/IGVFFI6792MVVQ/), [IGVFFI7980BYFW](/sequence-files/IGVFFI7980BYFW/), [IGVFFI8821XNHL](/sequence-files/IGVFFI8821XNHL/), [IGVFFI2454KXWO](/sequence-files/IGVFFI2454KXWO/), [IGVFFI3560UZZB](/sequence-files/IGVFFI3560UZZB/), [IGVFFI6942JVNS](/sequence-files/IGVFFI6942JVNS/), [IGVFFI7479JTPN](/sequence-files/IGVFFI7479JTPN/), [IGVFFI9650HDVE](/sequence-files/IGVFFI9650HDVE/), [IGVFFI1608WOSR](/sequence-files/IGVFFI1608WOSR/), [IGVFFI9346RSQU](/sequence-files/IGVFFI9346RSQU/), [IGVFFI4480XZFW](/sequence-files/IGVFFI4480XZFW/), [IGVFFI4339JATS](/sequence-files/IGVFFI4339JATS/), [IGVFFI4436RISI](/sequence-files/IGVFFI4436RISI/), [IGVFFI5971MRUB](/sequence-files/IGVFFI5971MRUB/), [IGVFFI7418XODT](/sequence-files/IGVFFI7418XODT/), [IGVFFI6307ZZKZ](/sequence-files/IGVFFI6307ZZKZ/), [IGVFFI9356QVZH](/sequence-files/IGVFFI9356QVZH/), [IGVFFI5579SHRT](/sequence-files/IGVFFI5579SHRT/), [IGVFFI4311QEZM](/sequence-files/IGVFFI4311QEZM/), [IGVFFI7665FNBQ](/sequence-files/IGVFFI7665FNBQ/), [IGVFFI9726EBVJ](/sequence-files/IGVFFI9726EBVJ/), [IGVFFI9601YCMM](/sequence-files/IGVFFI9601YCMM/) 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/IGVFDS6622DPIT/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS6622DPIT](/measurement-sets/IGVFDS6622DPIT/) 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/IGVFDS6622DPIT/"
}
]
},
"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": "2023-11-30T22:49:53.886807+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/IGVFFI1614ULLM/",
"accession": "IGVFFI1614ULLM",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep1-BinB-PCRrep9_I1"
],
"content_type": "reads",
"controlled_access": false,
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"md5sum": "0428657f5678f05deb0c8c6a4305b5fa",
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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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"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep1-BinB-PCRrep11_R1"
],
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},
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"upload_status": "validated"
},
{
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"accession": "IGVFFI0204LBGG",
"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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],
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},
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},
{
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},
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},
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},
{
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],
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},
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},
{
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],
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"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep1-BinB-PCRrep5_S209_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9601YCMM/",
"accession": "IGVFFI9601YCMM",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep1-BinB-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:40:47.897865+00:00",
"file_format": "fastq",
"file_size": 5458915,
"href": "/sequence-files/IGVFFI9601YCMM/@@download/IGVFFI9601YCMM.fastq.gz",
"md5sum": "5e13fa934d06691c365b899c9c82be9e",
"s3_uri": "s3://igvf-files/2023/12/05/36f8dbeb-56d1-470f-96e5-a6c62bce8669/IGVFFI9601YCMM.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-FFrep1-BinB-PCRrep1_S205_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": "2023-12-20T23:06:09.957011+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0143XZGF/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0143XZGF",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep1-BinB"
],
"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 26-50% 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": "2023-12-05T21:40:21.601688+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": "9a90c2e2-0b93-4c18-9115-d3fa96d61696"
}