{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0968GSSQ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0968GSSQ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinB_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 [IGVFSM8173RIRG](/in-vitro-systems/IGVFSM8173RIRG/) 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/IGVFSM8173RIRG/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM8173RIRG](/in-vitro-systems/IGVFSM8173RIRG/) 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/IGVFSM8173RIRG/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS0968GSSQ](/measurement-sets/IGVFDS0968GSSQ/) 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/IGVFDS0968GSSQ/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS0968GSSQ](/measurement-sets/IGVFDS0968GSSQ/) has sequence file(s) [IGVFFI5503JFHU](/sequence-files/IGVFFI5503JFHU/), [IGVFFI3731JIOR](/sequence-files/IGVFFI3731JIOR/), [IGVFFI0984RNPV](/sequence-files/IGVFFI0984RNPV/), [IGVFFI9012PVCM](/sequence-files/IGVFFI9012PVCM/), [IGVFFI8825JAVA](/sequence-files/IGVFFI8825JAVA/), [IGVFFI2317BDNL](/sequence-files/IGVFFI2317BDNL/), [IGVFFI6462UPBZ](/sequence-files/IGVFFI6462UPBZ/), [IGVFFI2451GGHM](/sequence-files/IGVFFI2451GGHM/) 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/IGVFDS0968GSSQ/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS0968GSSQ](/measurement-sets/IGVFDS0968GSSQ/) has sequence file(s): [IGVFFI5503JFHU](/sequence-files/IGVFFI5503JFHU/), [IGVFFI3731JIOR](/sequence-files/IGVFFI3731JIOR/), [IGVFFI0984RNPV](/sequence-files/IGVFFI0984RNPV/), [IGVFFI9012PVCM](/sequence-files/IGVFFI9012PVCM/), [IGVFFI8825JAVA](/sequence-files/IGVFFI8825JAVA/), [IGVFFI2317BDNL](/sequence-files/IGVFFI2317BDNL/), [IGVFFI6462UPBZ](/sequence-files/IGVFFI6462UPBZ/), [IGVFFI2451GGHM](/sequence-files/IGVFFI2451GGHM/) 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/IGVFDS0968GSSQ/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS0968GSSQ](/measurement-sets/IGVFDS0968GSSQ/) 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/IGVFDS0968GSSQ/"
}
]
},
"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": "2023-11-30T22:46:49.295727+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/IGVFFI5503JFHU/",
"accession": "IGVFFI5503JFHU",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinB-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:52:16.745709+00:00",
"file_format": "fastq",
"file_size": 19125981,
"href": "/sequence-files/IGVFFI5503JFHU/@@download/IGVFFI5503JFHU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/59f4e904-a49d-4f3c-b861-adb346d6433d/IGVFFI5503JFHU.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-BinB-PCRrep2_S126_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3731JIOR/",
"accession": "IGVFFI3731JIOR",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinB-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:39:24.739882+00:00",
"file_format": "fastq",
"file_size": 8994765,
"href": "/sequence-files/IGVFFI3731JIOR/@@download/IGVFFI3731JIOR.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/5290bd4f-2d0d-484e-b7d1-5bee3bdafc34/IGVFFI3731JIOR.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-BinB-PCRrep2_S126_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0984RNPV/",
"accession": "IGVFFI0984RNPV",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinB-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:04:54.457868+00:00",
"file_format": "fastq",
"file_size": 3127917,
"href": "/sequence-files/IGVFFI0984RNPV/@@download/IGVFFI0984RNPV.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/75da6e73-3101-4cd8-b8f1-01761bf664ac/IGVFFI0984RNPV.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-BinB-PCRrep2_S126_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9012PVCM/",
"accession": "IGVFFI9012PVCM",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinB-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:17:10.313500+00:00",
"file_format": "fastq",
"file_size": 3014242,
"href": "/sequence-files/IGVFFI9012PVCM/@@download/IGVFFI9012PVCM.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/5f3ceed5-6a8e-43f2-9bd8-f60fbb4bc0ad/IGVFFI9012PVCM.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-BinB-PCRrep2_S126_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8825JAVA/",
"accession": "IGVFFI8825JAVA",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinB-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:33:08.736148+00:00",
"file_format": "fastq",
"file_size": 8784578,
"href": "/sequence-files/IGVFFI8825JAVA/@@download/IGVFFI8825JAVA.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/840d6ed0-a8ab-47a5-810e-33fa9148e60c/IGVFFI8825JAVA.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-BinB-PCRrep1_S30_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2317BDNL/",
"accession": "IGVFFI2317BDNL",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinB-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:58:37.906479+00:00",
"file_format": "fastq",
"file_size": 3015030,
"href": "/sequence-files/IGVFFI2317BDNL/@@download/IGVFFI2317BDNL.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/37a0f4e5-faaa-439f-acf6-63bf2186951d/IGVFFI2317BDNL.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-BinB-PCRrep1_S30_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6462UPBZ/",
"accession": "IGVFFI6462UPBZ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinB-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:45:48.837121+00:00",
"file_format": "fastq",
"file_size": 17918527,
"href": "/sequence-files/IGVFFI6462UPBZ/@@download/IGVFFI6462UPBZ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/e9dbf619-b8bf-48b3-8424-e42dbce7e919/IGVFFI6462UPBZ.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-BinB-PCRrep1_S30_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2451GGHM/",
"accession": "IGVFFI2451GGHM",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinB-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:11:04.087488+00:00",
"file_format": "fastq",
"file_size": 2889453,
"href": "/sequence-files/IGVFFI2451GGHM/@@download/IGVFFI2451GGHM.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/7e26ea62-91a8-4289-b12b-085f506fca25/IGVFFI2451GGHM.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-BinB-PCRrep1_S30_I2_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": "2023-12-20T23:09:37.101232+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8173RIRG/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8173RIRG",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinB"
],
"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 11-20% 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": "2023-12-05T18:33:08.736148+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": "82302103-75ea-44cc-a454-7393e7c40197"
}