Single cell RNA sequencing (scRNAseq) technique is becoming increasingly popular for unbiased and high-resolutional transcriptome analysis of heterogeneous cell populations. Despite its many advantages, scRNAseq, like any other genomic sequencing technique, is susceptible to the influence of confounding effects. Controlling ...
Read More »Interesting Times in RNA Sequencing
A multi-institution research group jointly led by Professor Jan Prins and UNC CS alumna Professor Jinze Liu at the University of Kentucky is developing algorithms and software to analyze RNA using high-throughput sequencers. The software is in use in multiple ...
Read More »Developmental Analysis of Spliceosomal snRNA Isoform Expression with RNA-Seq
Pre-mRNA splicing is a critical step in eukaryotic gene expression that contributes to proteomic, cellular and developmental complexity. Small nuclear (sn)RNAs are core spliceosomal components, however, the extent to which differential expression of snRNA isoforms regulates splicing is completely unknown. ...
Read More »A novel multi-alignment pipeline for high-throughput sequencing data
Mapping reads to a reference sequence is a common step when analyzing allele effects in high-throughput sequencing data. The choice of reference is critical because its effect on quantitative sequence analysis is non-negligible. Recent studies suggest aligning to a single ...
Read More »Vicinal: a method for the determination of ncRNA ends using chimeric reads from RNA-seq experiments
Non-coding (nc)RNAs are important structural and regulatory molecules. Accurate determination of the primary sequence and secondary structure of ncRNAs is important for understanding their functions. During cDNA synthesis, RNA 3′ end stem-loops can self-prime reverse transcription, creating RNA-cDNA chimeras. Researchers ...
Read More »RIP-seq analysis of eukaryotic Sm proteins identifies three major categories of Sm-containing ribonucleoproteins
Sm proteins are multimeric RNA-binding factors, found in all three domains of life. Eukaryotic Sm proteins, together with their associated RNAs, form small ribonucleoprotein (RNP) complexes important in multiple aspects of gene regulation. Comprehensive knowledge of the RNA components of ...
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