{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7114WEPZ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7114WEPZ",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-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 [IGVFDS7114WEPZ](/measurement-sets/IGVFDS7114WEPZ/) has sequence file(s) [IGVFFI4033OVLA](/sequence-files/IGVFFI4033OVLA/), [IGVFFI9739MMIU](/sequence-files/IGVFFI9739MMIU/), [IGVFFI3229MNJP](/sequence-files/IGVFFI3229MNJP/), [IGVFFI3547UHDU](/sequence-files/IGVFFI3547UHDU/), [IGVFFI9601YPAU](/sequence-files/IGVFFI9601YPAU/), [IGVFFI4789ELUN](/sequence-files/IGVFFI4789ELUN/), [IGVFFI7267CIMW](/sequence-files/IGVFFI7267CIMW/), [IGVFFI7423TDGE](/sequence-files/IGVFFI7423TDGE/) 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/IGVFDS7114WEPZ/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7114WEPZ](/measurement-sets/IGVFDS7114WEPZ/) has sequence file(s): [IGVFFI4033OVLA](/sequence-files/IGVFFI4033OVLA/), [IGVFFI9739MMIU](/sequence-files/IGVFFI9739MMIU/), [IGVFFI3229MNJP](/sequence-files/IGVFFI3229MNJP/), [IGVFFI3547UHDU](/sequence-files/IGVFFI3547UHDU/), [IGVFFI9601YPAU](/sequence-files/IGVFFI9601YPAU/), [IGVFFI4789ELUN](/sequence-files/IGVFFI4789ELUN/), [IGVFFI7267CIMW](/sequence-files/IGVFFI7267CIMW/), [IGVFFI7423TDGE](/sequence-files/IGVFFI7423TDGE/) 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/IGVFDS7114WEPZ/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS7114WEPZ](/measurement-sets/IGVFDS7114WEPZ/) 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/IGVFDS7114WEPZ/"
}
]
},
"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": "2024-12-10T22:32:05.019144+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": [
{
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"accession": "IGVFFI4033OVLA",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep1-FFrep1-FACS_Input-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T00:32:39.243527+00:00",
"file_format": "fastq",
"file_size": 35152200,
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"s3_uri": "s3://igvf-files/2024/12/11/ea2f7548-0bd4-48a7-914a-6808e13092f3/IGVFFI4033OVLA.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
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"upload_status": "validated"
},
{
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"accession": "IGVFFI9739MMIU",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep1-FFrep1-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T00:35:55.059006+00:00",
"file_format": "fastq",
"file_size": 35682824,
"href": "/sequence-files/IGVFFI9739MMIU/@@download/IGVFFI9739MMIU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/97311dc2-2aee-4fa0-a45f-b5a7dce08dc8/IGVFFI9739MMIU.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_C11-Amp_PPIF_5splicesite-BioRep1-FFrep1-BinAll-PCRrep2_S983_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3229MNJP/",
"accession": "IGVFFI3229MNJP",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep1-FFrep1-FACS_Input-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T17:23:06.228534+00:00",
"file_format": "fastq",
"file_size": 30424923,
"href": "/sequence-files/IGVFFI3229MNJP/@@download/IGVFFI3229MNJP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/1197bac6-d386-45cb-a09f-316c6abbc156/IGVFFI3229MNJP.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_C11-Amp_PPIF_5splicesite-BioRep1-FFrep1-BinAll-PCRrep1_S971_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3547UHDU/",
"accession": "IGVFFI3547UHDU",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep1-FFrep1-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T17:25:26.165381+00:00",
"file_format": "fastq",
"file_size": 30630241,
"href": "/sequence-files/IGVFFI3547UHDU/@@download/IGVFFI3547UHDU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/a17f2f83-dbea-46f9-a6f0-4c7f134b9170/IGVFFI3547UHDU.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_C11-Amp_PPIF_5splicesite-BioRep1-FFrep1-BinAll-PCRrep2_S983_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9601YPAU/",
"accession": "IGVFFI9601YPAU",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep1-FFrep1-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T23:30:40.852869+00:00",
"file_format": "fastq",
"file_size": 11743232,
"href": "/sequence-files/IGVFFI9601YPAU/@@download/IGVFFI9601YPAU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/cb38b091-f7a9-4561-ba9c-b2951c04adbd/IGVFFI9601YPAU.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C11-Amp_PPIF_5splicesite-BioRep1-FFrep1-BinAll-PCRrep2_S983_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4789ELUN/",
"accession": "IGVFFI4789ELUN",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep1-FFrep1-FACS_Input-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T21:14:55.993092+00:00",
"file_format": "fastq",
"file_size": 11232458,
"href": "/sequence-files/IGVFFI4789ELUN/@@download/IGVFFI4789ELUN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/944a56d2-af2f-47ba-a5a2-a80963361edf/IGVFFI4789ELUN.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C11-Amp_PPIF_5splicesite-BioRep1-FFrep1-BinAll-PCRrep1_S971_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7267CIMW/",
"accession": "IGVFFI7267CIMW",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep1-FFrep1-FACS_Input-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T21:17:56.706879+00:00",
"file_format": "fastq",
"file_size": 12939067,
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"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C11-Amp_PPIF_5splicesite-BioRep1-FFrep1-BinAll-PCRrep2_S983_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7423TDGE/",
"accession": "IGVFFI7423TDGE",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep1-FFrep1-FACS_Input-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T23:27:33.630126+00:00",
"file_format": "fastq",
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C11-Amp_PPIF_5splicesite-BioRep1-FFrep1-BinAll-PCRrep1_S971_I2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS1132MKHT/"
],
"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/IGVFSM7040CAHB/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7040CAHB",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep1-FFrep1-FACS_Input"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS2432IDGC/",
"accession": "IGVFDS2432IDGC",
"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": "2024-12-11T00:32:39.243527+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": "08a89adb-da54-401d-a8e0-9112ffc201b1"
}