{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7692AEEW/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7692AEEW",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-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": "missing publication",
"detail": "Measurement set [IGVFDS7692AEEW](/measurement-sets/IGVFDS7692AEEW/) 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/IGVFDS7692AEEW/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS7692AEEW](/measurement-sets/IGVFDS7692AEEW/) has sequence file(s) [IGVFFI1744SDTY](/sequence-files/IGVFFI1744SDTY/), [IGVFFI7603MECS](/sequence-files/IGVFFI7603MECS/), [IGVFFI2198DHHX](/sequence-files/IGVFFI2198DHHX/), [IGVFFI5071UOGU](/sequence-files/IGVFFI5071UOGU/), [IGVFFI0791HGLP](/sequence-files/IGVFFI0791HGLP/), [IGVFFI7501IWYG](/sequence-files/IGVFFI7501IWYG/), [IGVFFI0732ZMPS](/sequence-files/IGVFFI0732ZMPS/), [IGVFFI6241CRAT](/sequence-files/IGVFFI6241CRAT/) 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/IGVFDS7692AEEW/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7692AEEW](/measurement-sets/IGVFDS7692AEEW/) has sequence file(s): [IGVFFI1744SDTY](/sequence-files/IGVFFI1744SDTY/), [IGVFFI7603MECS](/sequence-files/IGVFFI7603MECS/), [IGVFFI2198DHHX](/sequence-files/IGVFFI2198DHHX/), [IGVFFI5071UOGU](/sequence-files/IGVFFI5071UOGU/), [IGVFFI0791HGLP](/sequence-files/IGVFFI0791HGLP/), [IGVFFI7501IWYG](/sequence-files/IGVFFI7501IWYG/), [IGVFFI0732ZMPS](/sequence-files/IGVFFI0732ZMPS/), [IGVFFI6241CRAT](/sequence-files/IGVFFI6241CRAT/) 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/IGVFDS7692AEEW/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM9746ERJH](/in-vitro-systems/IGVFSM9746ERJH/) 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/IGVFSM9746ERJH/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM9746ERJH](/in-vitro-systems/IGVFSM9746ERJH/) 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/IGVFSM9746ERJH/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS7692AEEW](/measurement-sets/IGVFDS7692AEEW/) 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/IGVFDS7692AEEW/"
}
]
},
"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": "2023-11-30T22:46:14.052964+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/IGVFFI1744SDTY/",
"accession": "IGVFFI1744SDTY",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-BinF-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:08:13.804476+00:00",
"file_format": "fastq",
"file_size": 13604940,
"href": "/sequence-files/IGVFFI1744SDTY/@@download/IGVFFI1744SDTY.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/728f66b3-e89d-4058-a69a-9bcccc814d94/IGVFFI1744SDTY.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-6-D21-pPPIF-Amp-pPPIF-2-1-2-BinF_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7603MECS/",
"accession": "IGVFFI7603MECS",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-BinF-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:51:24.105504+00:00",
"file_format": "fastq",
"file_size": 15650574,
"href": "/sequence-files/IGVFFI7603MECS/@@download/IGVFFI7603MECS.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/76d4c0d8-c684-47dc-b1af-adca49c02ad8/IGVFFI7603MECS.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-6-D21-pPPIF-Amp-pPPIF-2-1-1-BinF_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2198DHHX/",
"accession": "IGVFFI2198DHHX",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-BinF-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:28:06.355463+00:00",
"file_format": "fastq",
"file_size": 43285799,
"href": "/sequence-files/IGVFFI2198DHHX/@@download/IGVFFI2198DHHX.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/86fdb16b-eaa5-4485-83e8-97d15a6f0acc/IGVFFI2198DHHX.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-6-D21-pPPIF-Amp-pPPIF-2-1-1-BinF_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5071UOGU/",
"accession": "IGVFFI5071UOGU",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-BinF-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:39:48.762433+00:00",
"file_format": "fastq",
"file_size": 78701330,
"href": "/sequence-files/IGVFFI5071UOGU/@@download/IGVFFI5071UOGU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/40acd377-5361-41fa-b0eb-99edc5202fc6/IGVFFI5071UOGU.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-6-D21-pPPIF-Amp-pPPIF-2-1-1-BinF_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0791HGLP/",
"accession": "IGVFFI0791HGLP",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-BinF-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:45:50.544578+00:00",
"file_format": "fastq",
"file_size": 71586541,
"href": "/sequence-files/IGVFFI0791HGLP/@@download/IGVFFI0791HGLP.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/8ca37ed5-ebbf-4893-ad77-9d42ff6cb2ec/IGVFFI0791HGLP.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-6-D21-pPPIF-Amp-pPPIF-2-1-2-BinF_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7501IWYG/",
"accession": "IGVFFI7501IWYG",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-BinF-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:33:49.881835+00:00",
"file_format": "fastq",
"file_size": 40013069,
"href": "/sequence-files/IGVFFI7501IWYG/@@download/IGVFFI7501IWYG.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/af229137-1a00-47d1-81c8-3b31ac66bba2/IGVFFI7501IWYG.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-6-D21-pPPIF-Amp-pPPIF-2-1-2-BinF_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0732ZMPS/",
"accession": "IGVFFI0732ZMPS",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-BinF-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:02:39.081438+00:00",
"file_format": "fastq",
"file_size": 14838507,
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"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-6-D21-pPPIF-Amp-pPPIF-2-1-1-BinF_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6241CRAT/",
"accession": "IGVFFI6241CRAT",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-BinF-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:57:07.201760+00:00",
"file_format": "fastq",
"file_size": 14557326,
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"s3_uri": "s3://igvf-files/2023/12/05/66ec2dd7-e724-43cf-a52d-daea0255eac1/IGVFFI6241CRAT.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-6-D21-pPPIF-Amp-pPPIF-2-1-2-BinF_I1_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": "2023-12-20T23:10:35.937171+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9746ERJH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9746ERJH",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-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": "2023-12-05T18:28:06.355463+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": "9f4dd707-a996-4c33-af6c-30f6443e8907"
}