| Title: |
In vitro comparison of vCircTrappist with CIRI2. |
| Authors: |
Alexis S. Chasseur; Maxime Bellefroid; Mathilde Galais; Meijiao Gong; Pierre Lombard; Sarah Mathieu; Amandine Pecquet; Estelle Plant; Camille Ponsard; Laure Vreux; Carlo Yague-Sanz; Benjamin G. Dewals; Nicolas A. Gillet; Benoît Muylkens; Carine M. Van Lint; Damien Coupeau |
| Publication Year: |
2025 |
| Subject Terms: |
Medicine; Microbiology; Genetics; Molecular Biology; Evolutionary Biology; Immunology; Infectious Diseases; Virology; Biological Sciences not elsewhere classified; +non%22">xlink "> non; unconventional splicing mechanisms; sanger sequencings validated; recent attention focused; obtained novel insights; initially anticipated due; identify backsplicing events; human pathogens belonging; existing datasets encompassing; conserved eukaryotic patterns; coding rnas play; viral infection cycles; viral genomes include; unique viral characteristics; rna sequencing data; developed bioinformatic tool; various viral families; bioinformatic pipeline tailored; families |
| Description: |
(A) Number of backsplice junctions discovered by vCircTrappist and CIRI2 from in vitro circRNA sequencing data. For each virus, the raw log2 number of unique backsplice junctions was measured. The count obtained using vCircTrappist is depicted in blue, while the count obtained using CIRI2 is depicted in red. (B) Comparison of vCircTrappist vs CIRI2 in multiple infection contexts. The barplots represent the number of identified unique backsplice junctions for each program. For vCircTrappist, we segregated the canonical from non-canonical backsplice junctions. (C) vCircTrappist vs CIRI2 coverage of circRNA reads on the HAdV C5 genome. vCircTrappist reads are mapped to the upper part of the graph, while CIRI2 reads are mapped below. The Y axis represents the coverage in circRNA reads per billion reads mapped to the viral genome. The X axis represents the positions on the genome in base pairs. (D; F) Analysis of the coverage obtained with vCircTrappist. The Y axis indicates the number of times individual reads have mapped to a specific backsplice junction. The X axis indicates the positions (in bp) where the circRNA are backspliced. The positions of the primers for subsequent RT-PCR confirmation are indicated by black arrows. (E; G) PCR confirmation of the loci that were identified by vCircTrappist. White arrows were placed at the expected band size to facilitate reading. The smears indicate the presence of alternative circRNA transcripts. The ladder is the SmartLadder from Eurogentec, the 1kb band is indicated on the Figure. |
| Document Type: |
still image |
| Language: |
unknown |
| Relation: |
https://figshare.com/articles/figure/_i_In_vitro_i_comparison_of_vCircTrappist_with_CIRI2_/30105341 |
| DOI: |
10.1371/journal.ppat.1013448.g003 |
| Availability: |
https://doi.org/10.1371/journal.ppat.1013448.g003; https://figshare.com/articles/figure/_i_In_vitro_i_comparison_of_vCircTrappist_with_CIRI2_/30105341 |
| Rights: |
CC BY 4.0 |
| Accession Number: |
edsbas.93421F08 |
| Database: |
BASE |