Projects per year
Abstract
Alternative cleavage and polyadenylation generates mRNA 3' isoforms in a cell type-specific manner. Due to finite available RNA sequencing data of organisms with vast cell type complexity, currently available gene annotation resources are incomplete, which poses significant challenges to the comprehensive interpretation and quantification of transcriptomes. In this chapter, we introduce 3'GAmES, a stand-alone computational pipeline for the identification and quantification of novel mRNA 3'end isoforms from 3'mRNA sequencing data. 3'GAmES expands available repositories and improves comprehensive gene-tag counting by cost-effective 3' mRNA sequencing, faithfully mirroring whole-transcriptome RNAseq measurements. By employing R and bash shell scripts (assembled in a Singularity container) 3'GAmES systematically augments cell type-specific 3' ends of RNA polymerase II transcripts and increases the sensitivity of quantitative gene expression profiling by 3' mRNA sequencing. Public access: https://github.com/AmeresLab/3-GAmES.git.
Original language | English |
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Title of host publication | mRNA 3' End Processing and Metabolism |
Editors | Bin Tian |
Place of Publication | Cambridge |
Publisher | Academic Press |
Chapter | 10 |
Pages | 205-223 |
Number of pages | 19 |
ISBN (Print) | 9780128235737 |
DOIs | |
Publication status | Published - 2021 |
Publication series
Series | Methods in Enzymology |
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Volume | 655 |
ISSN | 0076-6879 |
Austrian Fields of Science 2012
- 106005 Bioinformatics
- 106023 Molecular biology
Keywords
- Gene Expression Profiling
- High-Throughput Nucleotide Sequencing
- Molecular Sequence Annotation
- Polyadenylation
- RNA, Messenger/genetics
- Sequence Analysis, RNA
- Transcriptome
- RNA sequencing
- mRNA 3′ end formation
- 3′GAmES
- Gene expression
- Alternative polyadenylation
- Transcriptomics
- 3′ mRNA sequencing
- Gene annotation
Projects
- 2 Active
-
RiboTrace: Bridging temporal resolution gaps to dissect RNA silencing at the molecular and genomic scale
1/01/22 → 31/01/25
Project: Research funding
-
RNAdeco: decorating RNA for a purpose
Jantsch, M. F., Ameres, S. & Hofacker, I.
1/03/20 → 29/02/28
Project: Research funding