{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0126OPKX/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0126OPKX",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep3-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 [IGVFSM3254FGUG](/in-vitro-systems/IGVFSM3254FGUG/) 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/IGVFSM3254FGUG/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM3254FGUG](/in-vitro-systems/IGVFSM3254FGUG/) 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/IGVFSM3254FGUG/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS0126OPKX](/measurement-sets/IGVFDS0126OPKX/) 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/IGVFDS0126OPKX/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS0126OPKX](/measurement-sets/IGVFDS0126OPKX/) has sequence file(s) [IGVFFI9043LDKG](/sequence-files/IGVFFI9043LDKG/), [IGVFFI0341YDJV](/sequence-files/IGVFFI0341YDJV/), [IGVFFI8932VPVL](/sequence-files/IGVFFI8932VPVL/), [IGVFFI9374EMYB](/sequence-files/IGVFFI9374EMYB/), [IGVFFI4833XUVS](/sequence-files/IGVFFI4833XUVS/), [IGVFFI8746EKKV](/sequence-files/IGVFFI8746EKKV/), [IGVFFI0959QCIL](/sequence-files/IGVFFI0959QCIL/), [IGVFFI2312SPKC](/sequence-files/IGVFFI2312SPKC/) 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/IGVFDS0126OPKX/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS0126OPKX](/measurement-sets/IGVFDS0126OPKX/) has sequence file(s): [IGVFFI9043LDKG](/sequence-files/IGVFFI9043LDKG/), [IGVFFI0341YDJV](/sequence-files/IGVFFI0341YDJV/), [IGVFFI8932VPVL](/sequence-files/IGVFFI8932VPVL/), [IGVFFI9374EMYB](/sequence-files/IGVFFI9374EMYB/), [IGVFFI4833XUVS](/sequence-files/IGVFFI4833XUVS/), [IGVFFI8746EKKV](/sequence-files/IGVFFI8746EKKV/), [IGVFFI0959QCIL](/sequence-files/IGVFFI0959QCIL/), [IGVFFI2312SPKC](/sequence-files/IGVFFI2312SPKC/) 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/IGVFDS0126OPKX/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS0126OPKX](/measurement-sets/IGVFDS0126OPKX/) 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/IGVFDS0126OPKX/"
}
]
},
"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": "2023-11-30T22:46:04.160146+00:00",
"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/IGVFFI9043LDKG/",
"accession": "IGVFFI9043LDKG",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep3-BinC-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:55:25.821957+00:00",
"file_format": "fastq",
"file_size": 15316227,
"href": "/sequence-files/IGVFFI9043LDKG/@@download/IGVFFI9043LDKG.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/9b7a05ad-5a01-404d-a00c-4925c5c4a7f9/IGVFFI9043LDKG.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-4-D21-pPPIF-Amp-pPPIF-1-3-2-BinC_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0341YDJV/",
"accession": "IGVFFI0341YDJV",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep3-BinC-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:38:09.092177+00:00",
"file_format": "fastq",
"file_size": 69401260,
"href": "/sequence-files/IGVFFI0341YDJV/@@download/IGVFFI0341YDJV.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/2db70004-698d-448d-a2f2-f626d6f3ff9f/IGVFFI0341YDJV.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-4-D21-pPPIF-Amp-pPPIF-1-3-1-BinC_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8932VPVL/",
"accession": "IGVFFI8932VPVL",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep3-BinC-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:06:41.573810+00:00",
"file_format": "fastq",
"file_size": 14477090,
"href": "/sequence-files/IGVFFI8932VPVL/@@download/IGVFFI8932VPVL.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/7d2d2cb4-d7be-4831-92e2-f4798a1f56f2/IGVFFI8932VPVL.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-4-D21-pPPIF-Amp-pPPIF-1-3-2-BinC_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9374EMYB/",
"accession": "IGVFFI9374EMYB",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep3-BinC-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:01:06.941701+00:00",
"file_format": "fastq",
"file_size": 13075485,
"href": "/sequence-files/IGVFFI9374EMYB/@@download/IGVFFI9374EMYB.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/93e3ecc8-782e-4f08-951e-64a326a7fc2a/IGVFFI9374EMYB.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-4-D21-pPPIF-Amp-pPPIF-1-3-1-BinC_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4833XUVS/",
"accession": "IGVFFI4833XUVS",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep3-BinC-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:26:29.142213+00:00",
"file_format": "fastq",
"file_size": 38415722,
"href": "/sequence-files/IGVFFI4833XUVS/@@download/IGVFFI4833XUVS.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/e0fcaa43-02c6-4ac7-8ee4-9a8620992f9c/IGVFFI4833XUVS.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-4-D21-pPPIF-Amp-pPPIF-1-3-1-BinC_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8746EKKV/",
"accession": "IGVFFI8746EKKV",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep3-BinC-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:44:10.101573+00:00",
"file_format": "fastq",
"file_size": 77191598,
"href": "/sequence-files/IGVFFI8746EKKV/@@download/IGVFFI8746EKKV.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/49b3c0aa-c6e6-44b2-964d-a4facf7626a3/IGVFFI8746EKKV.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-4-D21-pPPIF-Amp-pPPIF-1-3-2-BinC_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0959QCIL/",
"accession": "IGVFFI0959QCIL",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep3-BinC-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:49:52.477918+00:00",
"file_format": "fastq",
"file_size": 13790997,
"href": "/sequence-files/IGVFFI0959QCIL/@@download/IGVFFI0959QCIL.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/91fd09ea-5303-48ad-9301-f8b449874016/IGVFFI0959QCIL.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-4-D21-pPPIF-Amp-pPPIF-1-3-1-BinC_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2312SPKC/",
"accession": "IGVFFI2312SPKC",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep3-BinC-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:32:13.276654+00:00",
"file_format": "fastq",
"file_size": 42566657,
"href": "/sequence-files/IGVFFI2312SPKC/@@download/IGVFFI2312SPKC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/315f7056-70c0-43e4-ad0a-7c88a6f6ffbc/IGVFFI2312SPKC.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-4-D21-pPPIF-Amp-pPPIF-1-3-2-BinC_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": "2023-12-20T23:10:25.621574+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3254FGUG/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3254FGUG",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep3-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 35-45% 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": "2023-12-05T18:26:29.142213+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": "bfbd80f1-2fef-4028-80aa-b77ef0d0e01e"
}