{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7850WHCP/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7850WHCP",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCAG-THP1-BioRep1-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 [IGVFDS7850WHCP](/measurement-sets/IGVFDS7850WHCP/) has sequence file(s) [IGVFFI4172XWYE](/sequence-files/IGVFFI4172XWYE/), [IGVFFI7445URTK](/sequence-files/IGVFFI7445URTK/), [IGVFFI3472PZPD](/sequence-files/IGVFFI3472PZPD/), [IGVFFI9328IDQI](/sequence-files/IGVFFI9328IDQI/), [IGVFFI9997FUHB](/sequence-files/IGVFFI9997FUHB/), [IGVFFI0569AIKS](/sequence-files/IGVFFI0569AIKS/), [IGVFFI0333AZCX](/sequence-files/IGVFFI0333AZCX/), [IGVFFI4503OALR](/sequence-files/IGVFFI4503OALR/) 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/IGVFDS7850WHCP/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7850WHCP](/measurement-sets/IGVFDS7850WHCP/) has sequence file(s): [IGVFFI4172XWYE](/sequence-files/IGVFFI4172XWYE/), [IGVFFI7445URTK](/sequence-files/IGVFFI7445URTK/), [IGVFFI3472PZPD](/sequence-files/IGVFFI3472PZPD/), [IGVFFI9328IDQI](/sequence-files/IGVFFI9328IDQI/), [IGVFFI9997FUHB](/sequence-files/IGVFFI9997FUHB/), [IGVFFI0569AIKS](/sequence-files/IGVFFI0569AIKS/), [IGVFFI0333AZCX](/sequence-files/IGVFFI0333AZCX/), [IGVFFI4503OALR](/sequence-files/IGVFFI4503OALR/) 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/IGVFDS7850WHCP/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS7850WHCP](/measurement-sets/IGVFDS7850WHCP/) 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/IGVFDS7850WHCP/"
}
]
},
"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/IGVFDS8210FQOO/",
"accession": "IGVFDS8210FQOO",
"aliases": [
"jesse-engreitz:THP1-PE2_Exp7_PPIF_5SpliceSite-IndividualVariantExp_NegControl_AmpliconSequencing"
],
"status": "preview"
}
],
"control_for": [],
"creation_timestamp": "2024-12-10T22:34:34.887972+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/IGVFFI4172XWYE/",
"accession": "IGVFFI4172XWYE",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCAG-THP1-BioRep1-FFrep1-FACS_Input-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T01:46:46.504367+00:00",
"file_format": "fastq",
"file_size": 46867124,
"href": "/sequence-files/IGVFFI4172XWYE/@@download/IGVFFI4172XWYE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/9a38f7f0-5062-4b46-9fba-77ed4cffd126/IGVFFI4172XWYE.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_C12-Amp_PPIF_5splicesite-BioRep1-FFrep1-BinAll-PCRrep1_S987_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7445URTK/",
"accession": "IGVFFI7445URTK",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCAG-THP1-BioRep1-FFrep1-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T16:34:48.525709+00:00",
"file_format": "fastq",
"file_size": 53953576,
"href": "/sequence-files/IGVFFI7445URTK/@@download/IGVFFI7445URTK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/14e93668-b990-4827-a3ce-6083bdc24534/IGVFFI7445URTK.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_C12-Amp_PPIF_5splicesite-BioRep1-FFrep1-BinAll-PCRrep2_S993_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3472PZPD/",
"accession": "IGVFFI3472PZPD",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCAG-THP1-BioRep1-FFrep1-FACS_Input-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T19:46:54.228598+00:00",
"file_format": "fastq",
"file_size": 40017108,
"href": "/sequence-files/IGVFFI3472PZPD/@@download/IGVFFI3472PZPD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/8ade1301-c001-42cc-b2aa-f72125cc7a08/IGVFFI3472PZPD.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_C12-Amp_PPIF_5splicesite-BioRep1-FFrep1-BinAll-PCRrep1_S987_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9328IDQI/",
"accession": "IGVFFI9328IDQI",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCAG-THP1-BioRep1-FFrep1-FACS_Input-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T21:59:10.742330+00:00",
"file_format": "fastq",
"file_size": 16789979,
"href": "/sequence-files/IGVFFI9328IDQI/@@download/IGVFFI9328IDQI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/700b3634-0960-4445-92cb-a57105901b6a/IGVFFI9328IDQI.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_C12-Amp_PPIF_5splicesite-BioRep1-FFrep1-BinAll-PCRrep1_S987_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9997FUHB/",
"accession": "IGVFFI9997FUHB",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCAG-THP1-BioRep1-FFrep1-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T19:49:59.269423+00:00",
"file_format": "fastq",
"file_size": 45492495,
"href": "/sequence-files/IGVFFI9997FUHB/@@download/IGVFFI9997FUHB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/191f6dfb-ecc7-4795-9951-1a8bf0726b51/IGVFFI9997FUHB.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_C12-Amp_PPIF_5splicesite-BioRep1-FFrep1-BinAll-PCRrep2_S993_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0569AIKS/",
"accession": "IGVFFI0569AIKS",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCAG-THP1-BioRep1-FFrep1-FACS_Input-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T22:02:12.414008+00:00",
"file_format": "fastq",
"file_size": 18542652,
"href": "/sequence-files/IGVFFI0569AIKS/@@download/IGVFFI0569AIKS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/c0ef3fb2-5eea-4c36-be87-ce03cab677af/IGVFFI0569AIKS.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_C12-Amp_PPIF_5splicesite-BioRep1-FFrep1-BinAll-PCRrep2_S993_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0333AZCX/",
"accession": "IGVFFI0333AZCX",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCAG-THP1-BioRep1-FFrep1-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-12T00:15:39.005094+00:00",
"file_format": "fastq",
"file_size": 17809262,
"href": "/sequence-files/IGVFFI0333AZCX/@@download/IGVFFI0333AZCX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/12/bf7dd54c-bd38-46b5-9b4f-ecdab666757a/IGVFFI0333AZCX.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_C12-Amp_PPIF_5splicesite-BioRep1-FFrep1-BinAll-PCRrep2_S993_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4503OALR/",
"accession": "IGVFFI4503OALR",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCAG-THP1-BioRep1-FFrep1-FACS_Input-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-12T00:12:26.389105+00:00",
"file_format": "fastq",
"file_size": 15195335,
"href": "/sequence-files/IGVFFI4503OALR/@@download/IGVFFI4503OALR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/12/2a97b3a9-90bd-40f2-b931-8ff21e120574/IGVFFI4503OALR.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_C12-Amp_PPIF_5splicesite-BioRep1-FFrep1-BinAll-PCRrep1_S987_I2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS8174BPPS/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"preferred_assay_title": "Variant-EFFECTS",
"protocols": [
"https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1"
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4190EMFX/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4190EMFX",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCAG-THP1-BioRep1-FFrep1-FACS_Input"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS6555EOZU/",
"accession": "IGVFDS6555EOZU",
"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": "2024-12-11T01:46:46.504367+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": "d46d39b1-c9d9-4057-a874-55ec7175042b"
}