{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7884ORHK/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7884ORHK",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep2-FFrep1-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 [IGVFDS7884ORHK](/measurement-sets/IGVFDS7884ORHK/) has sequence file(s) [IGVFFI7355TMEI](/sequence-files/IGVFFI7355TMEI/), [IGVFFI9783BTLB](/sequence-files/IGVFFI9783BTLB/), [IGVFFI8627MYCO](/sequence-files/IGVFFI8627MYCO/), [IGVFFI5509KIEG](/sequence-files/IGVFFI5509KIEG/), [IGVFFI0591CMUQ](/sequence-files/IGVFFI0591CMUQ/), [IGVFFI3196RIUJ](/sequence-files/IGVFFI3196RIUJ/), [IGVFFI6141FYXW](/sequence-files/IGVFFI6141FYXW/), [IGVFFI8866VLKO](/sequence-files/IGVFFI8866VLKO/) 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/IGVFDS7884ORHK/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7884ORHK](/measurement-sets/IGVFDS7884ORHK/) has sequence file(s): [IGVFFI7355TMEI](/sequence-files/IGVFFI7355TMEI/), [IGVFFI9783BTLB](/sequence-files/IGVFFI9783BTLB/), [IGVFFI8627MYCO](/sequence-files/IGVFFI8627MYCO/), [IGVFFI5509KIEG](/sequence-files/IGVFFI5509KIEG/), [IGVFFI0591CMUQ](/sequence-files/IGVFFI0591CMUQ/), [IGVFFI3196RIUJ](/sequence-files/IGVFFI3196RIUJ/), [IGVFFI6141FYXW](/sequence-files/IGVFFI6141FYXW/), [IGVFFI8866VLKO](/sequence-files/IGVFFI8866VLKO/) 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/IGVFDS7884ORHK/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS7884ORHK](/measurement-sets/IGVFDS7884ORHK/) 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/IGVFDS7884ORHK/"
}
]
},
"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": "2024-12-01T19:58:37.856827+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/IGVFFI7355TMEI/",
"accession": "IGVFFI7355TMEI",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep2-FFrep1-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T21:02:31.895308+00:00",
"file_format": "fastq",
"file_size": 49729893,
"href": "/sequence-files/IGVFFI7355TMEI/@@download/IGVFFI7355TMEI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/70aba2a0-a9e5-4055-84b9-5e61eec798e7/IGVFFI7355TMEI.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-FFrep1-BinAll-PCRrep2_S977_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9783BTLB/",
"accession": "IGVFFI9783BTLB",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep2-FFrep1-FACS_Input-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T20:59:30.316053+00:00",
"file_format": "fastq",
"file_size": 37765266,
"href": "/sequence-files/IGVFFI9783BTLB/@@download/IGVFFI9783BTLB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/e0c573b9-8321-44b3-b2a0-b1be713f13e0/IGVFFI9783BTLB.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-FFrep1-BinAll-PCRrep1_S965_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8627MYCO/",
"accession": "IGVFFI8627MYCO",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep2-FFrep1-FACS_Input-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T22:39:06.927639+00:00",
"file_format": "fastq",
"file_size": 12167096,
"href": "/sequence-files/IGVFFI8627MYCO/@@download/IGVFFI8627MYCO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/093c407e-7a2f-4165-b3b2-ecb9d6e6ca8a/IGVFFI8627MYCO.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-FFrep1-BinAll-PCRrep1_S965_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5509KIEG/",
"accession": "IGVFFI5509KIEG",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep2-FFrep1-FACS_Input-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T21:49:12.653146+00:00",
"file_format": "fastq",
"file_size": 32513120,
"href": "/sequence-files/IGVFFI5509KIEG/@@download/IGVFFI5509KIEG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/6a27132d-3020-4a0b-9e61-e85ab57af3d8/IGVFFI5509KIEG.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-FFrep1-BinAll-PCRrep1_S965_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0591CMUQ/",
"accession": "IGVFFI0591CMUQ",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep2-FFrep1-FACS_Input-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T22:42:14.628558+00:00",
"file_format": "fastq",
"file_size": 15807664,
"href": "/sequence-files/IGVFFI0591CMUQ/@@download/IGVFFI0591CMUQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/e121be99-b92e-47b0-9b72-01ddd411d436/IGVFFI0591CMUQ.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-FFrep1-BinAll-PCRrep2_S977_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3196RIUJ/",
"accession": "IGVFFI3196RIUJ",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep2-FFrep1-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T21:53:04.381627+00:00",
"file_format": "fastq",
"file_size": 42610617,
"href": "/sequence-files/IGVFFI3196RIUJ/@@download/IGVFFI3196RIUJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/3e6c61b7-0aea-4f2d-a575-d0586adb7718/IGVFFI3196RIUJ.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-FFrep1-BinAll-PCRrep2_S977_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6141FYXW/",
"accession": "IGVFFI6141FYXW",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep2-FFrep1-FACS_Input-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T23:23:40.969774+00:00",
"file_format": "fastq",
"file_size": 12399835,
"href": "/sequence-files/IGVFFI6141FYXW/@@download/IGVFFI6141FYXW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/9b18874b-d2e7-4cd1-a847-1ba6cd44f730/IGVFFI6141FYXW.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-FFrep1-BinAll-PCRrep1_S965_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8866VLKO/",
"accession": "IGVFFI8866VLKO",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep2-FFrep1-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T23:26:35.483975+00:00",
"file_format": "fastq",
"file_size": 16140792,
"href": "/sequence-files/IGVFFI8866VLKO/@@download/IGVFFI8866VLKO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/24b5475d-d768-4e0b-a6cd-192f2d03057c/IGVFFI8866VLKO.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-FFrep1-BinAll-PCRrep2_S977_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/IGVFSM5690YCKN/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5690YCKN",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep2-FFrep1-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": "2024-12-01T20:59:30.316053+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": "9b304d3d-99aa-4168-a113-58b28aff6375"
}