{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7974EEXF/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7974EEXF",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-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 [IGVFDS7974EEXF](/measurement-sets/IGVFDS7974EEXF/) has sequence file(s) [IGVFFI3346XMGR](/sequence-files/IGVFFI3346XMGR/), [IGVFFI4724XLES](/sequence-files/IGVFFI4724XLES/), [IGVFFI1007LOIF](/sequence-files/IGVFFI1007LOIF/), [IGVFFI1650UPWF](/sequence-files/IGVFFI1650UPWF/), [IGVFFI4587GHWU](/sequence-files/IGVFFI4587GHWU/), [IGVFFI7122OBWN](/sequence-files/IGVFFI7122OBWN/), [IGVFFI8950FBQL](/sequence-files/IGVFFI8950FBQL/), [IGVFFI9263MNZA](/sequence-files/IGVFFI9263MNZA/) 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/IGVFDS7974EEXF/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7974EEXF](/measurement-sets/IGVFDS7974EEXF/) has sequence file(s): [IGVFFI3346XMGR](/sequence-files/IGVFFI3346XMGR/), [IGVFFI4724XLES](/sequence-files/IGVFFI4724XLES/), [IGVFFI1007LOIF](/sequence-files/IGVFFI1007LOIF/), [IGVFFI1650UPWF](/sequence-files/IGVFFI1650UPWF/), [IGVFFI4587GHWU](/sequence-files/IGVFFI4587GHWU/), [IGVFFI7122OBWN](/sequence-files/IGVFFI7122OBWN/), [IGVFFI8950FBQL](/sequence-files/IGVFFI8950FBQL/), [IGVFFI9263MNZA](/sequence-files/IGVFFI9263MNZA/) 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/IGVFDS7974EEXF/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS7974EEXF](/measurement-sets/IGVFDS7974EEXF/) 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/IGVFDS7974EEXF/"
}
]
},
"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/IGVFDS4103BJLT/",
"accession": "IGVFDS4103BJLT",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-THP1-PE2_Exp4_NegControl_AmpliconSequencing"
],
"status": "preview"
}
],
"control_for": [],
"creation_timestamp": "2024-11-25T23:53:41.303112+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/IGVFFI3346XMGR/",
"accession": "IGVFFI3346XMGR",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep1-FACS_Input-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T07:12:03.650684+00:00",
"file_format": "fastq",
"file_size": 9581897,
"href": "/sequence-files/IGVFFI3346XMGR/@@download/IGVFFI3346XMGR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/eeb8fb50-99bd-41a7-aec3-97c6b857ae72/IGVFFI3346XMGR.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240426S024-Enhancer-THP1-PPIF_Enhancer_val_guides-Amp_PPIF_enhancer-BioRep2-FFrep1-BinAll-PCRrep1_S803_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4724XLES/",
"accession": "IGVFFI4724XLES",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep1-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T07:13:30.426185+00:00",
"file_format": "fastq",
"file_size": 10557571,
"href": "/sequence-files/IGVFFI4724XLES/@@download/IGVFFI4724XLES.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/c7b96160-cd1e-4e35-bb9a-fea9c3dddeb3/IGVFFI4724XLES.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240426S024-Enhancer-THP1-PPIF_Enhancer_val_guides-Amp_PPIF_enhancer-BioRep2-FFrep1-BinAll-PCRrep2_S812_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1007LOIF/",
"accession": "IGVFFI1007LOIF",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep1-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T09:56:23.058142+00:00",
"file_format": "fastq",
"file_size": 12271044,
"href": "/sequence-files/IGVFFI1007LOIF/@@download/IGVFFI1007LOIF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/20abd0cf-8a78-469a-b37b-1eff1aa2e70e/IGVFFI1007LOIF.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240426S024-Enhancer-THP1-PPIF_Enhancer_val_guides-Amp_PPIF_enhancer-BioRep2-FFrep1-BinAll-PCRrep2_S812_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1650UPWF/",
"accession": "IGVFFI1650UPWF",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep1-FACS_Input-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T09:53:25.198843+00:00",
"file_format": "fastq",
"file_size": 11181884,
"href": "/sequence-files/IGVFFI1650UPWF/@@download/IGVFFI1650UPWF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/f08a110b-3b26-4d8d-a220-cd15b4845689/IGVFFI1650UPWF.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240426S024-Enhancer-THP1-PPIF_Enhancer_val_guides-Amp_PPIF_enhancer-BioRep2-FFrep1-BinAll-PCRrep1_S803_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4587GHWU/",
"accession": "IGVFFI4587GHWU",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep1-FACS_Input-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T13:48:48.513975+00:00",
"file_format": "fastq",
"file_size": 4461885,
"href": "/sequence-files/IGVFFI4587GHWU/@@download/IGVFFI4587GHWU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/495fb2e9-451d-4a86-8ad1-4260b170dfa4/IGVFFI4587GHWU.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240426S024-Enhancer-THP1-PPIF_Enhancer_val_guides-Amp_PPIF_enhancer-BioRep2-FFrep1-BinAll-PCRrep2_S812_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7122OBWN/",
"accession": "IGVFFI7122OBWN",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep1-FACS_Input-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T13:45:51.872286+00:00",
"file_format": "fastq",
"file_size": 4017216,
"href": "/sequence-files/IGVFFI7122OBWN/@@download/IGVFFI7122OBWN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/9119dfd9-69dc-4277-b095-bdca05ad6e37/IGVFFI7122OBWN.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240426S024-Enhancer-THP1-PPIF_Enhancer_val_guides-Amp_PPIF_enhancer-BioRep2-FFrep1-BinAll-PCRrep1_S803_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8950FBQL/",
"accession": "IGVFFI8950FBQL",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep1-FACS_Input-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T17:44:16.616100+00:00",
"file_format": "fastq",
"file_size": 4034908,
"href": "/sequence-files/IGVFFI8950FBQL/@@download/IGVFFI8950FBQL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/81ea4e74-ccfa-4112-b32d-c23b3d0d2d7f/IGVFFI8950FBQL.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240426S024-Enhancer-THP1-PPIF_Enhancer_val_guides-Amp_PPIF_enhancer-BioRep2-FFrep1-BinAll-PCRrep1_S803_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9263MNZA/",
"accession": "IGVFFI9263MNZA",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep1-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T17:47:17.996348+00:00",
"file_format": "fastq",
"file_size": 4327893,
"href": "/sequence-files/IGVFFI9263MNZA/@@download/IGVFFI9263MNZA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/0737b382-1c6b-4877-ac38-eeb267cf2adc/IGVFFI9263MNZA.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240426S024-Enhancer-THP1-PPIF_Enhancer_val_guides-Amp_PPIF_enhancer-BioRep2-FFrep1-BinAll-PCRrep2_S812_I2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4833ZRTZ/"
],
"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/IGVFSM6465EIGT/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6465EIGT",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep1-FACS_Input"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS4955GEYO/",
"accession": "IGVFDS4955GEYO",
"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": "2024-11-26T07:12:03.650684+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": "a777aeec-78f2-44cf-8b06-fb45852ca261"
}