{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4078LMLS/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4078LMLS",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep2-FFrep2-FACS_Input_AmpliconSequencing"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"status": "released",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS4078LMLS](/measurement-sets/IGVFDS4078LMLS/) has sequence file(s) [IGVFFI2689GXHY](/sequence-files/IGVFFI2689GXHY/), [IGVFFI2748FYDD](/sequence-files/IGVFFI2748FYDD/), [IGVFFI3958EBIN](/sequence-files/IGVFFI3958EBIN/), [IGVFFI1615KPLI](/sequence-files/IGVFFI1615KPLI/), [IGVFFI9587NIZW](/sequence-files/IGVFFI9587NIZW/), [IGVFFI6149MVHY](/sequence-files/IGVFFI6149MVHY/), [IGVFFI7991LVMR](/sequence-files/IGVFFI7991LVMR/), [IGVFFI0545FANP](/sequence-files/IGVFFI0545FANP/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/measurement-sets/IGVFDS4078LMLS/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS4078LMLS](/measurement-sets/IGVFDS4078LMLS/) has sequence file(s): [IGVFFI2689GXHY](/sequence-files/IGVFFI2689GXHY/), [IGVFFI2748FYDD](/sequence-files/IGVFFI2748FYDD/), [IGVFFI3958EBIN](/sequence-files/IGVFFI3958EBIN/), [IGVFFI1615KPLI](/sequence-files/IGVFFI1615KPLI/), [IGVFFI9587NIZW](/sequence-files/IGVFFI9587NIZW/), [IGVFFI6149MVHY](/sequence-files/IGVFFI6149MVHY/), [IGVFFI7991LVMR](/sequence-files/IGVFFI7991LVMR/), [IGVFFI0545FANP](/sequence-files/IGVFFI0545FANP/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS4078LMLS/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS4078LMLS](/measurement-sets/IGVFDS4078LMLS/) 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/IGVFDS4078LMLS/"
}
]
},
"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"
},
"control_file_sets": [
{
"@id": "/measurement-sets/IGVFDS0861MZYT/",
"accession": "IGVFDS0861MZYT",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-PE2_Exp6_NegControl_AmpliconSequencing"
],
"status": "preview"
}
],
"control_for": [],
"creation_timestamp": "2024-12-01T19:58:58.290640+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/IGVFFI2689GXHY/",
"accession": "IGVFFI2689GXHY",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep2-FFrep2-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T23:36:55.501155+00:00",
"file_format": "fastq",
"file_size": 13360890,
"href": "/sequence-files/IGVFFI2689GXHY/@@download/IGVFFI2689GXHY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/93c9e7a1-f6af-4142-bde2-b5b435989c4b/IGVFFI2689GXHY.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_pool-Amp_PPIF_5splicesite-BioRep2-FFrep2-BinAll-PCRrep2_S978_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2748FYDD/",
"accession": "IGVFFI2748FYDD",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep2-FFrep2-FACS_Input-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T22:02:13.780546+00:00",
"file_format": "fastq",
"file_size": 30725367,
"href": "/sequence-files/IGVFFI2748FYDD/@@download/IGVFFI2748FYDD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/7ff723e7-eec6-4099-8da3-2e0b561f82ae/IGVFFI2748FYDD.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_pool-Amp_PPIF_5splicesite-BioRep2-FFrep2-BinAll-PCRrep1_S966_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3958EBIN/",
"accession": "IGVFFI3958EBIN",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep2-FFrep2-FACS_Input-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T21:10:05.355527+00:00",
"file_format": "fastq",
"file_size": 35400158,
"href": "/sequence-files/IGVFFI3958EBIN/@@download/IGVFFI3958EBIN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/7530d172-1478-428f-951e-86683703ee77/IGVFFI3958EBIN.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_pool-Amp_PPIF_5splicesite-BioRep2-FFrep2-BinAll-PCRrep1_S966_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1615KPLI/",
"accession": "IGVFFI1615KPLI",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep2-FFrep2-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T21:12:46.044957+00:00",
"file_format": "fastq",
"file_size": 40806431,
"href": "/sequence-files/IGVFFI1615KPLI/@@download/IGVFFI1615KPLI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/7bbd4f43-3e9e-46ad-83c5-f39570a6c46c/IGVFFI1615KPLI.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_pool-Amp_PPIF_5splicesite-BioRep2-FFrep2-BinAll-PCRrep2_S978_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9587NIZW/",
"accession": "IGVFFI9587NIZW",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep2-FFrep2-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T22:05:05.567046+00:00",
"file_format": "fastq",
"file_size": 34186776,
"href": "/sequence-files/IGVFFI9587NIZW/@@download/IGVFFI9587NIZW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/3503abac-534c-4c4f-9d6a-fbf2e5673414/IGVFFI9587NIZW.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_pool-Amp_PPIF_5splicesite-BioRep2-FFrep2-BinAll-PCRrep2_S978_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6149MVHY/",
"accession": "IGVFFI6149MVHY",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep2-FFrep2-FACS_Input-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T22:53:17.154483+00:00",
"file_format": "fastq",
"file_size": 13178026,
"href": "/sequence-files/IGVFFI6149MVHY/@@download/IGVFFI6149MVHY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/b9fe652c-af61-4777-bd52-29e7b0d6fb1d/IGVFFI6149MVHY.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_pool-Amp_PPIF_5splicesite-BioRep2-FFrep2-BinAll-PCRrep2_S978_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7991LVMR/",
"accession": "IGVFFI7991LVMR",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep2-FFrep2-FACS_Input-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T22:50:33.577031+00:00",
"file_format": "fastq",
"file_size": 11132442,
"href": "/sequence-files/IGVFFI7991LVMR/@@download/IGVFFI7991LVMR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/7bc9c5f6-c0c0-4be4-8a95-2952e367139b/IGVFFI7991LVMR.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_pool-Amp_PPIF_5splicesite-BioRep2-FFrep2-BinAll-PCRrep1_S966_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0545FANP/",
"accession": "IGVFFI0545FANP",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep2-FFrep2-FACS_Input-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T23:34:04.930222+00:00",
"file_format": "fastq",
"file_size": 11477064,
"href": "/sequence-files/IGVFFI0545FANP/@@download/IGVFFI0545FANP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/daaa0876-4222-47ef-9bd6-02ffbd8b44e0/IGVFFI0545FANP.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_pool-Amp_PPIF_5splicesite-BioRep2-FFrep2-BinAll-PCRrep1_S966_I2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS7090INDM/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"notes": "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"
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3000SOXC/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3000SOXC",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep2-FFrep2-FACS_Input"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS5639ITBS/",
"accession": "IGVFDS5639ITBS",
"file_set_type": "guide library",
"status": "preview",
"summary": "guide (sgRNA) library targeting sequence variants in a genomic locus"
}
],
"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": "preview",
"summary": "THP-1 cell line, male, Homo sapiens modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transfected with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "23",
"status": "preview",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2024-12-01T21:10:05.355527+00:00",
"summary": "CRISPR prime editing Variant-EFFECTS 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": [
"rotamase F",
"CYP3",
"cyclophilin F",
"mitochondrial cyclophilin",
"peptidyl-prolyl cis-trans isomerase, mitochondrial",
"CypD",
"Cyp-D",
"cyclophilin 3",
"cyclophilin D",
"CyP-M",
"peptidyl-prolyl cis-trans isomerase F, mitochondrial",
"PPIase F"
]
}
],
"uuid": "23e08716-5bcc-492f-b283-aba531492cf8"
}