{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0264KDQT/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0264KDQT",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-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 [IGVFDS0264KDQT](/measurement-sets/IGVFDS0264KDQT/) has sequence file(s) [IGVFFI0735CZIY](/sequence-files/IGVFFI0735CZIY/), [IGVFFI9546QSZV](/sequence-files/IGVFFI9546QSZV/), [IGVFFI0078FGMT](/sequence-files/IGVFFI0078FGMT/), [IGVFFI6499NANO](/sequence-files/IGVFFI6499NANO/), [IGVFFI7175LBAE](/sequence-files/IGVFFI7175LBAE/), [IGVFFI4775ABDM](/sequence-files/IGVFFI4775ABDM/), [IGVFFI3366HCNZ](/sequence-files/IGVFFI3366HCNZ/), [IGVFFI5307BEWY](/sequence-files/IGVFFI5307BEWY/) 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/IGVFDS0264KDQT/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS0264KDQT](/measurement-sets/IGVFDS0264KDQT/) has sequence file(s): [IGVFFI0735CZIY](/sequence-files/IGVFFI0735CZIY/), [IGVFFI9546QSZV](/sequence-files/IGVFFI9546QSZV/), [IGVFFI0078FGMT](/sequence-files/IGVFFI0078FGMT/), [IGVFFI6499NANO](/sequence-files/IGVFFI6499NANO/), [IGVFFI7175LBAE](/sequence-files/IGVFFI7175LBAE/), [IGVFFI4775ABDM](/sequence-files/IGVFFI4775ABDM/), [IGVFFI3366HCNZ](/sequence-files/IGVFFI3366HCNZ/), [IGVFFI5307BEWY](/sequence-files/IGVFFI5307BEWY/) 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/IGVFDS0264KDQT/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS0264KDQT](/measurement-sets/IGVFDS0264KDQT/) 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/IGVFDS0264KDQT/"
}
]
},
"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": "2024-11-25T23:52:21.905951+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/IGVFFI0735CZIY/",
"accession": "IGVFFI0735CZIY",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep1-FACS_Input-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T06:10:57.917481+00:00",
"file_format": "fastq",
"file_size": 10438073,
"href": "/sequence-files/IGVFFI0735CZIY/@@download/IGVFFI0735CZIY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/ee156b28-974f-4614-9402-6cc5542c3b6a/IGVFFI0735CZIY.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240426S024-Enhancer-THP1-PPIF_Enhancer_val_guides-Amp_PPIF_enhancer-BioRep1-FFrep1-BinAll-PCRrep1_S799_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9546QSZV/",
"accession": "IGVFFI9546QSZV",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep1-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T06:12:52.565742+00:00",
"file_format": "fastq",
"file_size": 10426622,
"href": "/sequence-files/IGVFFI9546QSZV/@@download/IGVFFI9546QSZV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/adc08edb-8806-4227-b9d4-fa3edf2e3f27/IGVFFI9546QSZV.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-BioRep1-FFrep1-BinAll-PCRrep2_S808_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0078FGMT/",
"accession": "IGVFFI0078FGMT",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep1-FACS_Input-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T08:13:38.392683+00:00",
"file_format": "fastq",
"file_size": 12032187,
"href": "/sequence-files/IGVFFI0078FGMT/@@download/IGVFFI0078FGMT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/38b277ae-e089-4c17-9eca-7d2a0b1ec30e/IGVFFI0078FGMT.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-BioRep1-FFrep1-BinAll-PCRrep1_S799_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6499NANO/",
"accession": "IGVFFI6499NANO",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep1-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T08:15:33.220486+00:00",
"file_format": "fastq",
"file_size": 12016331,
"href": "/sequence-files/IGVFFI6499NANO/@@download/IGVFFI6499NANO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/cdd3c11b-7fe3-4970-ac63-2ec02182a690/IGVFFI6499NANO.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-BioRep1-FFrep1-BinAll-PCRrep2_S808_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7175LBAE/",
"accession": "IGVFFI7175LBAE",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep1-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T15:46:48.237916+00:00",
"file_format": "fastq",
"file_size": 4472453,
"href": "/sequence-files/IGVFFI7175LBAE/@@download/IGVFFI7175LBAE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/329fefe1-f925-404a-baec-eaeb4f248a63/IGVFFI7175LBAE.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240426S024-Enhancer-THP1-PPIF_Enhancer_val_guides-Amp_PPIF_enhancer-BioRep1-FFrep1-BinAll-PCRrep2_S808_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4775ABDM/",
"accession": "IGVFFI4775ABDM",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep1-FACS_Input-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T11:48:21.012650+00:00",
"file_format": "fastq",
"file_size": 4817499,
"href": "/sequence-files/IGVFFI4775ABDM/@@download/IGVFFI4775ABDM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/79fb18cf-3244-432f-a433-adab1bdedecf/IGVFFI4775ABDM.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-BioRep1-FFrep1-BinAll-PCRrep1_S799_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3366HCNZ/",
"accession": "IGVFFI3366HCNZ",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep1-FACS_Input-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T11:51:51.936746+00:00",
"file_format": "fastq",
"file_size": 4550881,
"href": "/sequence-files/IGVFFI3366HCNZ/@@download/IGVFFI3366HCNZ.fastq.gz",
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"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240426S024-Enhancer-THP1-PPIF_Enhancer_val_guides-Amp_PPIF_enhancer-BioRep1-FFrep1-BinAll-PCRrep2_S808_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5307BEWY/",
"accession": "IGVFFI5307BEWY",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep1-FACS_Input-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T15:43:21.030709+00:00",
"file_format": "fastq",
"file_size": 4545419,
"href": "/sequence-files/IGVFFI5307BEWY/@@download/IGVFFI5307BEWY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/77fa2f3d-a394-458c-a017-129a184b7528/IGVFFI5307BEWY.fastq.gz",
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240426S024-Enhancer-THP1-PPIF_Enhancer_val_guides-Amp_PPIF_enhancer-BioRep1-FFrep1-BinAll-PCRrep1_S799_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/IGVFSM2936AUBH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2936AUBH",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-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": "2024-11-26T06:10:57.917481+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": "cb492e66-1159-4f79-bb31-b2f9836c3a6e"
}