{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7791SSYA/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7791SSYA",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-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 [IGVFSM8306UJIK](/in-vitro-systems/IGVFSM8306UJIK/) 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/IGVFSM8306UJIK/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM8306UJIK](/in-vitro-systems/IGVFSM8306UJIK/) 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/IGVFSM8306UJIK/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS7791SSYA](/measurement-sets/IGVFDS7791SSYA/) 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/IGVFDS7791SSYA/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS7791SSYA](/measurement-sets/IGVFDS7791SSYA/) has sequence file(s) [IGVFFI8641CGUF](/sequence-files/IGVFFI8641CGUF/), [IGVFFI1273FVOV](/sequence-files/IGVFFI1273FVOV/), [IGVFFI3404NXVD](/sequence-files/IGVFFI3404NXVD/), [IGVFFI6308LDQT](/sequence-files/IGVFFI6308LDQT/), [IGVFFI1924MRKT](/sequence-files/IGVFFI1924MRKT/), [IGVFFI0672DUJG](/sequence-files/IGVFFI0672DUJG/), [IGVFFI0489WMTS](/sequence-files/IGVFFI0489WMTS/), [IGVFFI6802UZJD](/sequence-files/IGVFFI6802UZJD/), [IGVFFI2357GFRP](/sequence-files/IGVFFI2357GFRP/), [IGVFFI6471UCND](/sequence-files/IGVFFI6471UCND/), [IGVFFI7224IOUE](/sequence-files/IGVFFI7224IOUE/), [IGVFFI9021TMRZ](/sequence-files/IGVFFI9021TMRZ/), [IGVFFI9292VWLO](/sequence-files/IGVFFI9292VWLO/), [IGVFFI2672OWHW](/sequence-files/IGVFFI2672OWHW/), [IGVFFI5987TFNZ](/sequence-files/IGVFFI5987TFNZ/), [IGVFFI1657ZNTX](/sequence-files/IGVFFI1657ZNTX/), [IGVFFI9027PTOT](/sequence-files/IGVFFI9027PTOT/), [IGVFFI2934ZXGD](/sequence-files/IGVFFI2934ZXGD/), [IGVFFI9114VVAZ](/sequence-files/IGVFFI9114VVAZ/), [IGVFFI4525QYYH](/sequence-files/IGVFFI4525QYYH/), [IGVFFI4540IATW](/sequence-files/IGVFFI4540IATW/), [IGVFFI4210OBHK](/sequence-files/IGVFFI4210OBHK/), [IGVFFI9652SUQL](/sequence-files/IGVFFI9652SUQL/), [IGVFFI7710GJOY](/sequence-files/IGVFFI7710GJOY/), [IGVFFI3789BUHG](/sequence-files/IGVFFI3789BUHG/), [IGVFFI6474WNZU](/sequence-files/IGVFFI6474WNZU/), [IGVFFI7688YMGF](/sequence-files/IGVFFI7688YMGF/), [IGVFFI8743XBVZ](/sequence-files/IGVFFI8743XBVZ/), [IGVFFI5071ECFV](/sequence-files/IGVFFI5071ECFV/), [IGVFFI2379NLON](/sequence-files/IGVFFI2379NLON/), [IGVFFI2293DXED](/sequence-files/IGVFFI2293DXED/), [IGVFFI9817TCOP](/sequence-files/IGVFFI9817TCOP/), [IGVFFI1823DGHM](/sequence-files/IGVFFI1823DGHM/), [IGVFFI1209LYPN](/sequence-files/IGVFFI1209LYPN/), [IGVFFI1285FBAY](/sequence-files/IGVFFI1285FBAY/), [IGVFFI0266YLEF](/sequence-files/IGVFFI0266YLEF/), [IGVFFI6779SYGX](/sequence-files/IGVFFI6779SYGX/), [IGVFFI7850JTBF](/sequence-files/IGVFFI7850JTBF/), [IGVFFI4376PGVF](/sequence-files/IGVFFI4376PGVF/), [IGVFFI9534RDYC](/sequence-files/IGVFFI9534RDYC/), [IGVFFI0817NXQZ](/sequence-files/IGVFFI0817NXQZ/), [IGVFFI4504YLHO](/sequence-files/IGVFFI4504YLHO/), [IGVFFI2521TPAQ](/sequence-files/IGVFFI2521TPAQ/), [IGVFFI9454CBLL](/sequence-files/IGVFFI9454CBLL/), [IGVFFI2905KIJB](/sequence-files/IGVFFI2905KIJB/), [IGVFFI3978QDWV](/sequence-files/IGVFFI3978QDWV/), [IGVFFI8501HHMY](/sequence-files/IGVFFI8501HHMY/), [IGVFFI1163QCXS](/sequence-files/IGVFFI1163QCXS/) 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/IGVFDS7791SSYA/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7791SSYA](/measurement-sets/IGVFDS7791SSYA/) has sequence file(s): [IGVFFI8641CGUF](/sequence-files/IGVFFI8641CGUF/), [IGVFFI1273FVOV](/sequence-files/IGVFFI1273FVOV/), [IGVFFI3404NXVD](/sequence-files/IGVFFI3404NXVD/), [IGVFFI6308LDQT](/sequence-files/IGVFFI6308LDQT/), [IGVFFI1924MRKT](/sequence-files/IGVFFI1924MRKT/), [IGVFFI0672DUJG](/sequence-files/IGVFFI0672DUJG/), [IGVFFI0489WMTS](/sequence-files/IGVFFI0489WMTS/), [IGVFFI6802UZJD](/sequence-files/IGVFFI6802UZJD/), [IGVFFI2357GFRP](/sequence-files/IGVFFI2357GFRP/), [IGVFFI6471UCND](/sequence-files/IGVFFI6471UCND/), [IGVFFI7224IOUE](/sequence-files/IGVFFI7224IOUE/), [IGVFFI9021TMRZ](/sequence-files/IGVFFI9021TMRZ/), [IGVFFI9292VWLO](/sequence-files/IGVFFI9292VWLO/), [IGVFFI2672OWHW](/sequence-files/IGVFFI2672OWHW/), [IGVFFI5987TFNZ](/sequence-files/IGVFFI5987TFNZ/), [IGVFFI1657ZNTX](/sequence-files/IGVFFI1657ZNTX/), [IGVFFI9027PTOT](/sequence-files/IGVFFI9027PTOT/), [IGVFFI2934ZXGD](/sequence-files/IGVFFI2934ZXGD/), [IGVFFI9114VVAZ](/sequence-files/IGVFFI9114VVAZ/), [IGVFFI4525QYYH](/sequence-files/IGVFFI4525QYYH/), [IGVFFI4540IATW](/sequence-files/IGVFFI4540IATW/), [IGVFFI4210OBHK](/sequence-files/IGVFFI4210OBHK/), [IGVFFI9652SUQL](/sequence-files/IGVFFI9652SUQL/), [IGVFFI7710GJOY](/sequence-files/IGVFFI7710GJOY/), [IGVFFI3789BUHG](/sequence-files/IGVFFI3789BUHG/), [IGVFFI6474WNZU](/sequence-files/IGVFFI6474WNZU/), [IGVFFI7688YMGF](/sequence-files/IGVFFI7688YMGF/), [IGVFFI8743XBVZ](/sequence-files/IGVFFI8743XBVZ/), [IGVFFI5071ECFV](/sequence-files/IGVFFI5071ECFV/), [IGVFFI2379NLON](/sequence-files/IGVFFI2379NLON/), [IGVFFI2293DXED](/sequence-files/IGVFFI2293DXED/), [IGVFFI9817TCOP](/sequence-files/IGVFFI9817TCOP/), [IGVFFI1823DGHM](/sequence-files/IGVFFI1823DGHM/), [IGVFFI1209LYPN](/sequence-files/IGVFFI1209LYPN/), [IGVFFI1285FBAY](/sequence-files/IGVFFI1285FBAY/), [IGVFFI0266YLEF](/sequence-files/IGVFFI0266YLEF/), [IGVFFI6779SYGX](/sequence-files/IGVFFI6779SYGX/), [IGVFFI7850JTBF](/sequence-files/IGVFFI7850JTBF/), [IGVFFI4376PGVF](/sequence-files/IGVFFI4376PGVF/), [IGVFFI9534RDYC](/sequence-files/IGVFFI9534RDYC/), [IGVFFI0817NXQZ](/sequence-files/IGVFFI0817NXQZ/), [IGVFFI4504YLHO](/sequence-files/IGVFFI4504YLHO/), [IGVFFI2521TPAQ](/sequence-files/IGVFFI2521TPAQ/), [IGVFFI9454CBLL](/sequence-files/IGVFFI9454CBLL/), [IGVFFI2905KIJB](/sequence-files/IGVFFI2905KIJB/), [IGVFFI3978QDWV](/sequence-files/IGVFFI3978QDWV/), [IGVFFI8501HHMY](/sequence-files/IGVFFI8501HHMY/), [IGVFFI1163QCXS](/sequence-files/IGVFFI1163QCXS/) 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/IGVFDS7791SSYA/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS7791SSYA](/measurement-sets/IGVFDS7791SSYA/) 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/IGVFDS7791SSYA/"
}
]
},
"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": "2023-12-01T00:05:35.075223+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/IGVFFI8641CGUF/",
"accession": "IGVFFI8641CGUF",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-BinC-PCRrep9_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:51:04.423775+00:00",
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"file_size": 10601517,
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"md5sum": "13b1b30198cf273224f8979e11bb38b2",
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"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1273FVOV/",
"accession": "IGVFFI1273FVOV",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-BinC-PCRrep1_R2"
],
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3404NXVD/",
"accession": "IGVFFI3404NXVD",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-BinC-PCRrep4_I1"
],
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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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"accession": "IGVFFI1924MRKT",
"aliases": [
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],
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0672DUJG/",
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"aliases": [
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],
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},
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},
{
"@id": "/sequence-files/IGVFFI0489WMTS/",
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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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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2357GFRP/",
"accession": "IGVFFI2357GFRP",
"aliases": [
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],
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6471UCND/",
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"aliases": [
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],
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"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-BinC-PCRrep1_S25_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1163QCXS/",
"accession": "IGVFFI1163QCXS",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-BinC-PCRrep3_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:47:05.417884+00:00",
"file_format": "fastq",
"file_size": 2619732,
"href": "/sequence-files/IGVFFI1163QCXS/@@download/IGVFFI1163QCXS.fastq.gz",
"md5sum": "92659bf9ae747a4a8e6a891e3fbf985b",
"s3_uri": "s3://igvf-files/2023/12/05/ffb5665d-f42b-4ab6-90f0-0be6f049e19a/IGVFFI1163QCXS.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-FFrep1-BinC-PCRrep3_S27_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": "2023-12-20T23:06:13.176992+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8306UJIK/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8306UJIK",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-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": "2023-12-05T19:44:08.838460+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": "8e998d76-8027-4694-8050-b9815a5e9652"
}