{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3999GGTI/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3999GGTI",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep1-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 [IGVFDS3999GGTI](/measurement-sets/IGVFDS3999GGTI/) has sequence file(s) [IGVFFI3411GTKY](/sequence-files/IGVFFI3411GTKY/), [IGVFFI7038ZRKI](/sequence-files/IGVFFI7038ZRKI/), [IGVFFI8041TXSD](/sequence-files/IGVFFI8041TXSD/), [IGVFFI8430EHHS](/sequence-files/IGVFFI8430EHHS/), [IGVFFI6752NQPD](/sequence-files/IGVFFI6752NQPD/), [IGVFFI2361LSRG](/sequence-files/IGVFFI2361LSRG/), [IGVFFI1342DZHT](/sequence-files/IGVFFI1342DZHT/), [IGVFFI7201MBBR](/sequence-files/IGVFFI7201MBBR/) 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/IGVFDS3999GGTI/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS3999GGTI](/measurement-sets/IGVFDS3999GGTI/) has sequence file(s): [IGVFFI3411GTKY](/sequence-files/IGVFFI3411GTKY/), [IGVFFI7038ZRKI](/sequence-files/IGVFFI7038ZRKI/), [IGVFFI8041TXSD](/sequence-files/IGVFFI8041TXSD/), [IGVFFI8430EHHS](/sequence-files/IGVFFI8430EHHS/), [IGVFFI6752NQPD](/sequence-files/IGVFFI6752NQPD/), [IGVFFI2361LSRG](/sequence-files/IGVFFI2361LSRG/), [IGVFFI1342DZHT](/sequence-files/IGVFFI1342DZHT/), [IGVFFI7201MBBR](/sequence-files/IGVFFI7201MBBR/) 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/IGVFDS3999GGTI/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS3999GGTI](/measurement-sets/IGVFDS3999GGTI/) 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/IGVFDS3999GGTI/"
}
]
},
"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": "2024-12-01T19:58:18.606466+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/IGVFFI3411GTKY/",
"accession": "IGVFFI3411GTKY",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep1-FFrep2-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T20:51:31.826648+00:00",
"file_format": "fastq",
"file_size": 51528503,
"href": "/sequence-files/IGVFFI3411GTKY/@@download/IGVFFI3411GTKY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/80d98196-4060-45cb-a708-d4d06655433a/IGVFFI3411GTKY.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-BioRep1-FFrep2-BinAll-PCRrep2_S976_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7038ZRKI/",
"accession": "IGVFFI7038ZRKI",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep1-FFrep2-FACS_Input-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T20:48:07.472000+00:00",
"file_format": "fastq",
"file_size": 38985376,
"href": "/sequence-files/IGVFFI7038ZRKI/@@download/IGVFFI7038ZRKI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/9d638bec-112d-4d76-9485-c9cf8e6e3aff/IGVFFI7038ZRKI.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-BioRep1-FFrep2-BinAll-PCRrep1_S964_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8041TXSD/",
"accession": "IGVFFI8041TXSD",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep1-FFrep2-FACS_Input-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T21:33:19.829382+00:00",
"file_format": "fastq",
"file_size": 33018453,
"href": "/sequence-files/IGVFFI8041TXSD/@@download/IGVFFI8041TXSD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/7a8806b6-b64f-447c-b09c-a113ee909229/IGVFFI8041TXSD.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-BioRep1-FFrep2-BinAll-PCRrep1_S964_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8430EHHS/",
"accession": "IGVFFI8430EHHS",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep1-FFrep2-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T21:37:58.967684+00:00",
"file_format": "fastq",
"file_size": 41958637,
"href": "/sequence-files/IGVFFI8430EHHS/@@download/IGVFFI8430EHHS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/849a1f9a-49d8-46d1-9fee-fffc2b5e86bb/IGVFFI8430EHHS.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-BioRep1-FFrep2-BinAll-PCRrep2_S976_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6752NQPD/",
"accession": "IGVFFI6752NQPD",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep1-FFrep2-FACS_Input-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T22:29:05.223521+00:00",
"file_format": "fastq",
"file_size": 16653130,
"href": "/sequence-files/IGVFFI6752NQPD/@@download/IGVFFI6752NQPD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/70507587-be54-4a91-871e-86a8370f7c23/IGVFFI6752NQPD.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-BioRep1-FFrep2-BinAll-PCRrep2_S976_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2361LSRG/",
"accession": "IGVFFI2361LSRG",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep1-FFrep2-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T23:15:41.486109+00:00",
"file_format": "fastq",
"file_size": 16104820,
"href": "/sequence-files/IGVFFI2361LSRG/@@download/IGVFFI2361LSRG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/d12132fc-3262-4e1e-aebe-e4cf025c4f2c/IGVFFI2361LSRG.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-BioRep1-FFrep2-BinAll-PCRrep2_S976_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1342DZHT/",
"accession": "IGVFFI1342DZHT",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep1-FFrep2-FACS_Input-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T22:24:06.462144+00:00",
"file_format": "fastq",
"file_size": 13123542,
"href": "/sequence-files/IGVFFI1342DZHT/@@download/IGVFFI1342DZHT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/4fca530a-185f-4f1b-9f4c-7c2d22834043/IGVFFI1342DZHT.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-BioRep1-FFrep2-BinAll-PCRrep1_S964_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7201MBBR/",
"accession": "IGVFFI7201MBBR",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep1-FFrep2-FACS_Input-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T23:12:19.087447+00:00",
"file_format": "fastq",
"file_size": 12310556,
"href": "/sequence-files/IGVFFI7201MBBR/@@download/IGVFFI7201MBBR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/75c4e2b7-4507-47ae-8670-019d6c8b9d6e/IGVFFI7201MBBR.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-BioRep1-FFrep2-BinAll-PCRrep1_S964_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/IGVFSM7914DVZT/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7914DVZT",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep1-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": "2024-12-01T20:48:07.472000+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": "fabcd918-ad78-4dfe-bd4c-bbc4917701eb"
}