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Phospho-RNAseq Profiling of Extracellular mRNAs and lncRNAs
2021Extracellular RNAs (exRNAs) in biofluids have attracted great interest as potential biomarkers. Although extracellular microRNAs in blood plasma are extensively characterized, extracellular messenger RNA (mRNA) and long noncoding RNA (lncRNA) studies are limited. We have recently reported that human plasma contains fragmented mRNAs and lncRNAs that are
Maria D, Giraldez, Muneesh, Tewari
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Single-Cell RNAseq Data QC and Preprocessing
2022The first step in single-cell RNAseq data analysis is the evaluation of the overall quality of the cell transcriptome and the preparation of the single-cell transcription data for clustering. In this chapter, we describe one of the possible approaches to perform single-cell data preprocessing for 3' end single-cell RNAseq transcriptomics data.
Olivero, Martina, Calogero, Raffaele A
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Bioinformatic Pipelines to Analyze lncRNAs RNAseq Data
2021RNA-sequencing could be nowadays considered the gold standard to study the coding and noncoding transcriptome. The great advantage of high-throughput sequencing in the characterization and quantification of long noncoding RNA (lncRNA) resides in its capability to capture the complexity of lncRNA transcripts configuration patterns, even in the presence ...
Luca, Agnelli +2 more
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Quantifying alternative polyadenylation in RNAseq data with LABRAT
2021Alternative polyadenylation (APA) generates transcript isoforms that differ in their 3' UTR content and may therefore be subject to different regulatory fates. Although the existence of APA has been known for decades, quantification of APA isoforms from high-throughput RNA sequencing data has been difficult.
Austin E, Gillen +2 more
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RNAseqâbased phylogenetic reconstruction of Taxaceae and Cephalotaxaceae
Cladistics, 2018AbstractTaxaceae and Cephalotaxaceae are the two economically important conifer families. Over the years there has been much controversy over the issue of merging these families. The position of Amentotaxus and Torreya is also ambiguous. Some authors consider them closer to Taxaceae while others deemed them to fit within Cephalotaxaceae.
Aasim Majeed +3 more
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Integration of ENCODE RNAseq and eCLIP Data Sets
2017During the last decade, the study of mRNA decay has largely benefited from an increasing number of high-throughput assays that emerged from developments in next generation sequencing (NGS) technologies as well as mass spectrometry. While assay-specific data analysis is often reported and software made available many researchers struggle with the ...
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RNAseq data analysis using Galaxy
2017This is a bioinformatics exercise intended for use in a computer lab setting with life science majors.
Escobar, Matthew +4 more
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