Custom long non-coding RNA capture enhances detection sensitivity in different human sample types.
Annelien MorlionCeline EveraertJustine NuytensEva HulstaertJo VandesompelePieter MestdaghPublished in: RNA biology (2021)
Long non-coding RNAs (lncRNAs) are a heterogeneous group of transcripts that lack protein coding potential and display regulatory functions in various cellular processes. As a result of their cell- and cancer-specific expression patterns, lncRNAs have emerged as potential diagnostic and therapeutic targets. The accurate characterization of lncRNAs in bulk transcriptome data remains challenging due to their low abundance compared to protein coding genes. To tackle this issue, we describe a unique short-read custom lncRNA capture sequencing approach that relies on a comprehensive set of 565,878 capture probes for 49,372 human lncRNA genes. This custom lncRNA capture approach was evaluated on various sample types ranging from artificial high-quality RNA mixtures to more challenging formalin-fixed paraffin-embedded tissue and biofluid material. The custom enrichment approach allows the detection of a more diverse repertoire of lncRNAs, with better reproducibility and higher coverage compared to classic total RNA-sequencing.
Keyphrases
- long non coding rna
- poor prognosis
- single cell
- genome wide identification
- genome wide analysis
- endothelial cells
- rna seq
- genome wide
- network analysis
- transcription factor
- induced pluripotent stem cells
- pluripotent stem cells
- binding protein
- papillary thyroid
- high resolution
- gene expression
- loop mediated isothermal amplification
- dna methylation
- single molecule
- protein protein
- electronic health record
- machine learning
- human health
- mass spectrometry
- real time pcr
- risk assessment
- label free
- nucleic acid
- climate change
- antibiotic resistance genes
- sensitive detection
- deep learning
- data analysis
- wastewater treatment
- childhood cancer