{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7434URBG/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7434URBG",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-BinF_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 [IGVFSM3596XEKI](/in-vitro-systems/IGVFSM3596XEKI/) 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/IGVFSM3596XEKI/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM3596XEKI](/in-vitro-systems/IGVFSM3596XEKI/) 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/IGVFSM3596XEKI/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS7434URBG](/measurement-sets/IGVFDS7434URBG/) 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/IGVFDS7434URBG/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS7434URBG](/measurement-sets/IGVFDS7434URBG/) has sequence file(s) [IGVFFI0105BAVC](/sequence-files/IGVFFI0105BAVC/), [IGVFFI9112BOOJ](/sequence-files/IGVFFI9112BOOJ/), [IGVFFI7044OWCL](/sequence-files/IGVFFI7044OWCL/), [IGVFFI7123KDWL](/sequence-files/IGVFFI7123KDWL/), [IGVFFI3178KUPW](/sequence-files/IGVFFI3178KUPW/), [IGVFFI6876IPUR](/sequence-files/IGVFFI6876IPUR/), [IGVFFI6003HJIN](/sequence-files/IGVFFI6003HJIN/), [IGVFFI1163VEBI](/sequence-files/IGVFFI1163VEBI/) 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/IGVFDS7434URBG/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7434URBG](/measurement-sets/IGVFDS7434URBG/) has sequence file(s): [IGVFFI0105BAVC](/sequence-files/IGVFFI0105BAVC/), [IGVFFI9112BOOJ](/sequence-files/IGVFFI9112BOOJ/), [IGVFFI7044OWCL](/sequence-files/IGVFFI7044OWCL/), [IGVFFI7123KDWL](/sequence-files/IGVFFI7123KDWL/), [IGVFFI3178KUPW](/sequence-files/IGVFFI3178KUPW/), [IGVFFI6876IPUR](/sequence-files/IGVFFI6876IPUR/), [IGVFFI6003HJIN](/sequence-files/IGVFFI6003HJIN/), [IGVFFI1163VEBI](/sequence-files/IGVFFI1163VEBI/) 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/IGVFDS7434URBG/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS7434URBG](/measurement-sets/IGVFDS7434URBG/) 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/IGVFDS7434URBG/"
}
]
},
"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": "2023-11-30T22:46:00.154610+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/IGVFFI0105BAVC/",
"accession": "IGVFFI0105BAVC",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-BinF-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:43:29.788436+00:00",
"file_format": "fastq",
"file_size": 76011296,
"href": "/sequence-files/IGVFFI0105BAVC/@@download/IGVFFI0105BAVC.fastq.gz",
"md5sum": "10fb71832a555bc63256baddd7e4969b",
"s3_uri": "s3://igvf-files/2023/12/05/c09e220e-77e2-4524-8fae-1fb76255fb21/IGVFFI0105BAVC.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-3-D21-pPPIF-Amp-pPPIF-1-2-2-BinF_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9112BOOJ/",
"accession": "IGVFFI9112BOOJ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-BinF-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:49:15.668355+00:00",
"file_format": "fastq",
"file_size": 14523840,
"href": "/sequence-files/IGVFFI9112BOOJ/@@download/IGVFFI9112BOOJ.fastq.gz",
"md5sum": "79292aa4a2f5d1ceee3c6d13392110bf",
"s3_uri": "s3://igvf-files/2023/12/05/605711fe-b471-4a78-8146-3fde2d335a3b/IGVFFI9112BOOJ.fastq.gz",
"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-BinF_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7044OWCL/",
"accession": "IGVFFI7044OWCL",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-BinF-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:00:30.253795+00:00",
"file_format": "fastq",
"file_size": 13210710,
"href": "/sequence-files/IGVFFI7044OWCL/@@download/IGVFFI7044OWCL.fastq.gz",
"md5sum": "ea3af7c77d4f3c9745bc5988ff6f88ca",
"s3_uri": "s3://igvf-files/2023/12/05/2bc79c2b-81ad-475a-b6ab-9800257a7bfa/IGVFFI7044OWCL.fastq.gz",
"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-BinF_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7123KDWL/",
"accession": "IGVFFI7123KDWL",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-BinF-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:37:26.705182+00:00",
"file_format": "fastq",
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"href": "/sequence-files/IGVFFI7123KDWL/@@download/IGVFFI7123KDWL.fastq.gz",
"md5sum": "b800394fa86d3d7d0d97f763b0c9cb11",
"s3_uri": "s3://igvf-files/2023/12/05/bceae66f-ecef-4117-818d-1889a35cbd30/IGVFFI7123KDWL.fastq.gz",
"sequencing_platform": {
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3178KUPW/",
"accession": "IGVFFI3178KUPW",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-BinF-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:06:04.457570+00:00",
"file_format": "fastq",
"file_size": 14413778,
"href": "/sequence-files/IGVFFI3178KUPW/@@download/IGVFFI3178KUPW.fastq.gz",
"md5sum": "1b340a9646a6a2484ada3d2120e460df",
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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-1-2-2-BinF_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6876IPUR/",
"accession": "IGVFFI6876IPUR",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-BinF-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:54:49.290571+00:00",
"file_format": "fastq",
"file_size": 15209970,
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"md5sum": "2177f200284d8872b879de9d492dde97",
"s3_uri": "s3://igvf-files/2023/12/05/738315d2-ec53-4bd8-b477-19cc5d757ae7/IGVFFI6876IPUR.fastq.gz",
"sequencing_platform": {
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"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-3-D21-pPPIF-Amp-pPPIF-1-2-2-BinF_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6003HJIN/",
"accession": "IGVFFI6003HJIN",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-BinF-PCRrep2_R1"
],
"content_type": "reads",
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"creation_timestamp": "2023-12-05T18:31:36.028962+00:00",
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"md5sum": "7f1f7db23f4d4a948db8109651eaf7e5",
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},
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"submitted_file_name": "220228pPPIF-FFSample-3-D21-pPPIF-Amp-pPPIF-1-2-2-BinF_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1163VEBI/",
"accession": "IGVFFI1163VEBI",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-BinF-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:25:51.940970+00:00",
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"md5sum": "0b952368c4b531e73b11895802a7db62",
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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-BinF_R1_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": "2023-12-20T23:10:05.659443+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3596XEKI/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3596XEKI",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-BinF"
],
"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 90-100% 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": "2023-12-05T18:25:51.940970+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": "5df179b4-eb65-455e-b761-974779918f2b"
}