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GSE215252

GSE GEO
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FLARE: A fast and flexible peak-calling pipeline for identifying RNA editing foci

Organism: Homo sapiens
Platform: GPL24676
Samples: 3
Experiment Types:
Other
Submitted: Oct 11 2022
Last Updated: May 03 2024
Status: Public on Oct 18 2023
Contact: Gene,,Yeo (UCSD)

Relations

BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA889435

Summary

Experimental methods for discovering RNA Binding Protein (RBP) binding sites on target RNAs have recently emerged which employ fusions of RBPs to RNA-editing enzymes (such asAPOBEC1 or ADAR) to “label” mRNA. However, off-target editing, genetic variants and sequencing errors can lead to false positives when using data derived from such approaches, and highlight a need for a robust, statistical approach to prioritizing confident binding sites.

Overall Design

Transiently transfected RBFOX2-APOBEC1 fusion construct expression was induced in HEK293 cells using doxycycline for 72 hours before samples were prepared for RNA sequencing. We present FLagging Areas of RNA-editing Enrichment (FLARE), a Snakemake-based pipeline that uses a statistical approach to determine regions of enriched RNA editing, using SAILOR-derived editing sites as a starting point.

Analysis (5 steps)

View Data Processing
Processing steps for GSE215252
  1. STAR aligned original fastqs to hg19 reference build
  2. Run SAILOR to identify editing sites.
  3. Code available at: https://github.com/YeoLab/FLARE
  4. Run FLARE to identify regions of enriched editing.
  5. Code available at: https://github.com/YeoLab/FLARE

Supplementary Files (1)

GSE215252_RAW.tar Download
GEO Samples (3)
GSM6630377 GSM6630378 GSM6630379

Dataset Citations (1)

FLARE: a fast and flexible workflow for identifying RNA editing foci.
PMID 37784060 · 2023 · BMC bioinformatics
Eric Kofman, Brian Yee, Hugo C Medina-Munoz, Gene W Yeo

SRA Experiments (3) and Runs (3)

Total: 386 MB
SRX17851523 SRP402007 RNA-Seq SINGLE
GSM6630377: HEK293T cells, dox-induced RBFOX2-Apobec fusion replicate 1; Homo sapiens; RNA-Seq
Sample: SRS15373062
BioProject: PRJNA889435
BioSample: SAMN31244033
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: HEK293XT
cell line: HEK293XT
cell type: Human embryonic kidney
genotype: WT
treatment: Transient transfection
time: 72 hrs
geo_loc_name: missing
collection_date: missing
Original files (1)
HEK293XT
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR21863812 14772586 1452310766 145.59 RBFOX2_APO_rep1.fastqTr.sorted.STARUnmapped.out.sorted.STARAligned.ou… SRA
SRX17851524 SRP402007 RNA-Seq SINGLE
GSM6630378: HEK293T cells, dox-induced RBFOX2-Apobec fusion replicate 2; Homo sapiens; RNA-Seq
Sample: SRS15373063
BioProject: PRJNA889435
BioSample: SAMN31244032
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: HEK293XT
cell line: HEK293XT
cell type: Human embryonic kidney
genotype: WT
treatment: Transient transfection
time: 72 hrs
geo_loc_name: missing
collection_date: missing
Original files (1)
HEK293XT
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR21863811 15153671 1502298577 142.83 RBFOX2_APO_rep2.fastqTr.sorted.STARUnmapped.out.sorted.STARAligned.ou… SRA
SRX17851525 SRP402007 RNA-Seq SINGLE
GSM6630379: HEK293T cells, dox-induced RBFOX2-Apobec fusion replicate 3; Homo sapiens; RNA-Seq
Sample: SRS15373064
BioProject: PRJNA889435
BioSample: SAMN31244031
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: HEK293XT
cell line: HEK293XT
cell type: Human embryonic kidney
genotype: WT
treatment: Transient transfection
time: 72hrs
geo_loc_name: missing
collection_date: missing
Original files (1)
HEK293XT
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR21863810 11043775 1090083970 97.98 RBFOX2_APO_rep3.fastqTr.sorted.STARUnmapped.out.sorted.STARAligned.ou… SRA

Linked Publications (3)

Expanded palette of RNA base editors for comprehensive RBP-RNA interactome studies.
Nature communications · 2024
FLARE: a fast and flexible workflow for identifying RNA editing foci.
BMC bioinformatics · 2023
FLARE: a fast and flexible workflow for identifying RNA editing foci.
BMC bioinformatics · 2023

Data Files (9)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— RBFOX2_APO_rep1.fastqTr.sorted.STARUnmapped.out.sorted… RNA-Seq 145.6 MB link
— RBFOX2_APO_rep1.fastqTr.sorted.STARUnmapped.out.sorted… RNA-Seq 145.6 MB link
— RBFOX2_APO_rep1.fastqTr.sorted.STARUnmapped.out.sorted… RNA-Seq 145.6 MB link
— RBFOX2_APO_rep2.fastqTr.sorted.STARUnmapped.out.sorted… RNA-Seq 142.8 MB link
— RBFOX2_APO_rep2.fastqTr.sorted.STARUnmapped.out.sorted… RNA-Seq 142.8 MB link
— RBFOX2_APO_rep2.fastqTr.sorted.STARUnmapped.out.sorted… RNA-Seq 142.8 MB link
— RBFOX2_APO_rep3.fastqTr.sorted.STARUnmapped.out.sorted… RNA-Seq 98.0 MB link
— RBFOX2_APO_rep3.fastqTr.sorted.STARUnmapped.out.sorted… RNA-Seq 98.0 MB link
— RBFOX2_APO_rep3.fastqTr.sorted.STARUnmapped.out.sorted… RNA-Seq 98.0 MB link