{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0592EWPO/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0592EWPO",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-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 [IGVFSM9849CZIJ](/in-vitro-systems/IGVFSM9849CZIJ/) 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/IGVFSM9849CZIJ/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM9849CZIJ](/in-vitro-systems/IGVFSM9849CZIJ/) 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/IGVFSM9849CZIJ/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS0592EWPO](/measurement-sets/IGVFDS0592EWPO/) 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/IGVFDS0592EWPO/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS0592EWPO](/measurement-sets/IGVFDS0592EWPO/) has sequence file(s) [IGVFFI4308OYZA](/sequence-files/IGVFFI4308OYZA/), [IGVFFI6799LNKH](/sequence-files/IGVFFI6799LNKH/), [IGVFFI0267HTVT](/sequence-files/IGVFFI0267HTVT/), [IGVFFI0056CLSN](/sequence-files/IGVFFI0056CLSN/), [IGVFFI8378VHJA](/sequence-files/IGVFFI8378VHJA/), [IGVFFI7320NGYM](/sequence-files/IGVFFI7320NGYM/), [IGVFFI6562BTTV](/sequence-files/IGVFFI6562BTTV/), [IGVFFI4233FOVJ](/sequence-files/IGVFFI4233FOVJ/) 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/IGVFDS0592EWPO/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS0592EWPO](/measurement-sets/IGVFDS0592EWPO/) has sequence file(s): [IGVFFI4308OYZA](/sequence-files/IGVFFI4308OYZA/), [IGVFFI6799LNKH](/sequence-files/IGVFFI6799LNKH/), [IGVFFI0267HTVT](/sequence-files/IGVFFI0267HTVT/), [IGVFFI0056CLSN](/sequence-files/IGVFFI0056CLSN/), [IGVFFI8378VHJA](/sequence-files/IGVFFI8378VHJA/), [IGVFFI7320NGYM](/sequence-files/IGVFFI7320NGYM/), [IGVFFI6562BTTV](/sequence-files/IGVFFI6562BTTV/), [IGVFFI4233FOVJ](/sequence-files/IGVFFI4233FOVJ/) 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/IGVFDS0592EWPO/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS0592EWPO](/measurement-sets/IGVFDS0592EWPO/) 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/IGVFDS0592EWPO/"
}
]
},
"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": "2023-11-30T22:46:52.568306+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/IGVFFI4308OYZA/",
"accession": "IGVFFI4308OYZA",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinF-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:11:38.308221+00:00",
"file_format": "fastq",
"file_size": 2821743,
"href": "/sequence-files/IGVFFI4308OYZA/@@download/IGVFFI4308OYZA.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/4973da58-ab65-4ff7-a75b-aa88471dd845/IGVFFI4308OYZA.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220426pPPIF_REPEAT-THP1-Gen8b-pPPIF-Amp_pPPIF-BioRep2-FFRep2-BinF-PCRrep1_S34_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6799LNKH/",
"accession": "IGVFFI6799LNKH",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinF-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:46:25.297756+00:00",
"file_format": "fastq",
"file_size": 16106621,
"href": "/sequence-files/IGVFFI6799LNKH/@@download/IGVFFI6799LNKH.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/b3e3aacd-d6bf-481c-9955-3d8570025928/IGVFFI6799LNKH.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220426pPPIF_REPEAT-THP1-Gen8b-pPPIF-Amp_pPPIF-BioRep2-FFRep2-BinF-PCRrep1_S34_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0267HTVT/",
"accession": "IGVFFI0267HTVT",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinF-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:59:12.682998+00:00",
"file_format": "fastq",
"file_size": 2925283,
"href": "/sequence-files/IGVFFI0267HTVT/@@download/IGVFFI0267HTVT.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/f2657820-aaa2-4fc7-8a2f-6dd58882ee57/IGVFFI0267HTVT.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220426pPPIF_REPEAT-THP1-Gen8b-pPPIF-Amp_pPPIF-BioRep2-FFRep2-BinF-PCRrep1_S34_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0056CLSN/",
"accession": "IGVFFI0056CLSN",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinF-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:05:28.429372+00:00",
"file_format": "fastq",
"file_size": 3028664,
"href": "/sequence-files/IGVFFI0056CLSN/@@download/IGVFFI0056CLSN.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/beee96ea-6840-4350-95bd-a96d2cd62c96/IGVFFI0056CLSN.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220426pPPIF_REPEAT-THP1-Gen8b-pPPIF-Amp_pPPIF-BioRep2-FFRep2-BinF-PCRrep2_S130_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8378VHJA/",
"accession": "IGVFFI8378VHJA",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinF-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:52:57.326936+00:00",
"file_format": "fastq",
"file_size": 16898195,
"href": "/sequence-files/IGVFFI8378VHJA/@@download/IGVFFI8378VHJA.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/bf503dfb-71f6-4134-b2ca-0ddad19051c5/IGVFFI8378VHJA.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220426pPPIF_REPEAT-THP1-Gen8b-pPPIF-Amp_pPPIF-BioRep2-FFRep2-BinF-PCRrep2_S130_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7320NGYM/",
"accession": "IGVFFI7320NGYM",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinF-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:17:44.890038+00:00",
"file_format": "fastq",
"file_size": 2945204,
"href": "/sequence-files/IGVFFI7320NGYM/@@download/IGVFFI7320NGYM.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/8f3145a9-55c9-422a-974e-94a24a240858/IGVFFI7320NGYM.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220426pPPIF_REPEAT-THP1-Gen8b-pPPIF-Amp_pPPIF-BioRep2-FFRep2-BinF-PCRrep2_S130_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6562BTTV/",
"accession": "IGVFFI6562BTTV",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinF-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:40:00.759000+00:00",
"file_format": "fastq",
"file_size": 8499686,
"href": "/sequence-files/IGVFFI6562BTTV/@@download/IGVFFI6562BTTV.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/015d51f3-fcb2-4bf7-8b92-163c3f1a5eba/IGVFFI6562BTTV.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220426pPPIF_REPEAT-THP1-Gen8b-pPPIF-Amp_pPPIF-BioRep2-FFRep2-BinF-PCRrep2_S130_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4233FOVJ/",
"accession": "IGVFFI4233FOVJ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinF-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:33:44.681153+00:00",
"file_format": "fastq",
"file_size": 8287053,
"href": "/sequence-files/IGVFFI4233FOVJ/@@download/IGVFFI4233FOVJ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/fe69c161-7a4f-4c9f-b381-d8b239286f5a/IGVFFI4233FOVJ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220426pPPIF_REPEAT-THP1-Gen8b-pPPIF-Amp_pPPIF-BioRep2-FFRep2-BinF-PCRrep1_S34_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": "2023-12-20T23:09:28.774998+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9849CZIJ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9849CZIJ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-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": "2023-12-05T18:33:44.681153+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": "b6cbc731-883c-4c4e-9d52-e6d92b38a004"
}