{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4043NWWM/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4043NWWM",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-BinE_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 [IGVFDS4043NWWM](/measurement-sets/IGVFDS4043NWWM/) 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/IGVFDS4043NWWM/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS4043NWWM](/measurement-sets/IGVFDS4043NWWM/) has sequence file(s) [IGVFFI7603WROH](/sequence-files/IGVFFI7603WROH/), [IGVFFI9639APSP](/sequence-files/IGVFFI9639APSP/), [IGVFFI3785VNPS](/sequence-files/IGVFFI3785VNPS/), [IGVFFI2609XNGM](/sequence-files/IGVFFI2609XNGM/), [IGVFFI8418BNEE](/sequence-files/IGVFFI8418BNEE/), [IGVFFI9832DPPE](/sequence-files/IGVFFI9832DPPE/), [IGVFFI9507EESM](/sequence-files/IGVFFI9507EESM/), [IGVFFI6486WHWZ](/sequence-files/IGVFFI6486WHWZ/) 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/IGVFDS4043NWWM/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS4043NWWM](/measurement-sets/IGVFDS4043NWWM/) has sequence file(s): [IGVFFI7603WROH](/sequence-files/IGVFFI7603WROH/), [IGVFFI9639APSP](/sequence-files/IGVFFI9639APSP/), [IGVFFI3785VNPS](/sequence-files/IGVFFI3785VNPS/), [IGVFFI2609XNGM](/sequence-files/IGVFFI2609XNGM/), [IGVFFI8418BNEE](/sequence-files/IGVFFI8418BNEE/), [IGVFFI9832DPPE](/sequence-files/IGVFFI9832DPPE/), [IGVFFI9507EESM](/sequence-files/IGVFFI9507EESM/), [IGVFFI6486WHWZ](/sequence-files/IGVFFI6486WHWZ/) 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/IGVFDS4043NWWM/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM9337QVAD](/in-vitro-systems/IGVFSM9337QVAD/) has in progress subobject construct library set [IGVFDS6377KNCH](/construct-library-sets/IGVFDS6377KNCH/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM9337QVAD/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM9337QVAD](/in-vitro-systems/IGVFSM9337QVAD/) 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/IGVFSM9337QVAD/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS4043NWWM](/measurement-sets/IGVFDS4043NWWM/) 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/IGVFDS4043NWWM/"
}
]
},
"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/IGVFDS6377KNCH/",
"accession": "IGVFDS6377KNCH",
"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/IGVFDS6385JXFZ/",
"accession": "IGVFDS6385JXFZ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-THP1-PE2_Exp3_NegControl_AmpliconSequencing"
],
"status": "released"
}
],
"control_for": [],
"creation_timestamp": "2023-11-30T22:45:59.057254+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": "IGVFFI7603WROH",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-BinE-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:25:42.709182+00:00",
"file_format": "fastq",
"file_size": 41710700,
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"md5sum": "9a0c81247c2fa7757072d3a094e71b7a",
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"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-3-D21-pPPIF-Amp-pPPIF-1-2-1-BinE_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9639APSP/",
"accession": "IGVFFI9639APSP",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-BinE-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:31:26.759579+00:00",
"file_format": "fastq",
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"href": "/sequence-files/IGVFFI9639APSP/@@download/IGVFFI9639APSP.fastq.gz",
"md5sum": "b65d4863b8ecb1669b126e954f10107a",
"s3_uri": "s3://igvf-files/2023/12/05/63025699-9e9c-433c-add7-826cb816c6f5/IGVFFI9639APSP.fastq.gz",
"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/IGVFFI3785VNPS/",
"accession": "IGVFFI3785VNPS",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-BinE-PCRrep2_R2"
],
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"creation_timestamp": "2023-12-05T18:43:20.338113+00:00",
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"md5sum": "9a2febb7afa0f9abc960c977352d1490",
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"sequencing_platform": {
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"status": "released",
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2609XNGM/",
"accession": "IGVFFI2609XNGM",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-BinE-PCRrep1_I1"
],
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"controlled_access": false,
"creation_timestamp": "2023-12-05T18:49:06.674941+00:00",
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},
{
"@id": "/sequence-files/IGVFFI8418BNEE/",
"accession": "IGVFFI8418BNEE",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-BinE-PCRrep1_I2"
],
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"controlled_access": false,
"creation_timestamp": "2023-12-05T19:00:21.045874+00:00",
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9832DPPE/",
"accession": "IGVFFI9832DPPE",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-BinE-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:05:55.357628+00:00",
"file_format": "fastq",
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"md5sum": "79d765637165d926e300cc423f653a94",
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"sequencing_platform": {
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"term_name": "Illumina NextSeq 550"
},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9507EESM/",
"accession": "IGVFFI9507EESM",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-BinE-PCRrep2_I1"
],
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"term_name": "Illumina NextSeq 550"
},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6486WHWZ/",
"accession": "IGVFFI6486WHWZ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-BinE-PCRrep1_R2"
],
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-3-D21-pPPIF-Amp-pPPIF-1-2-1-BinE_R2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS5056OAGR/"
],
"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": "2023-12-20T23:09:10.374007+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9337QVAD/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9337QVAD",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-BinE"
],
"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 80-90% 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": "2023-12-05T18:25:42.709182+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": "330d97e4-e9c2-4843-9e2b-84960e8d901b"
}