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A detailed protocol for stranded RNA-sequencing

A detailed protocol for stranded RNA-sequencing

RNA-sequencing is a revolutionary tool to follow differential expression after treatment with cancer chemopreventive agents. It allows a real genome-wide screening independent of prior assumptions and is well suited for analyzing coding but also long noncoding RNAs. It still consents ...

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dRNA-Seq – Riboswitch Discovery by Combining RNA-Seq and Genome-Wide Identification of Transcriptional Start Sites

dRNA-Seq – Riboswitch Discovery by Combining RNA-Seq and Genome-Wide Identification of Transcriptional Start Sites

Deep-sequencing technologies applied to RNA have tremendous potential to identify novel transcripts with single-nucleotide resolution. By combining whole-transcript cDNA sequencing (RNA-seq) and genome-wide identification of transcription start sites (dRNA-seq), it is possible to characterize long 5′-untranslated regions potentially endowed with ...

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Computer-assisted annotation of small RNA transcriptomes

Computer-assisted annotation of small RNA transcriptomes

Small noncoding RNAs (sncRNAs) are widely expressed in the cell of almost all known species. Most sncRNAs appear to have regulatory roles, ranging from facilitating RNA production and modifications (e.g., snoRNAs) to control of mRNA stability and translational efficiency (e.g., ...

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Transcription Start Site Associated RNAs (TSSaRNAs) Are Ubiquitous in All Domains of Life

Transcription Start Site Associated RNAs (TSSaRNAs) Are Ubiquitous in All Domains of Life

A plethora of non-coding RNAs has been discovered using high-resolution transcriptomics tools, indicating that transcriptional and post-transcriptional regulation is much more complex than previously appreciated. Small RNAs associated with transcription start sites of annotated coding regions (TSSaRNAs) are pervasive in ...

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RNA-Seq of the Nucleolus Reveals Abundant SNORD44-Derived Small RNAs

RNA-Seq of the Nucleolus Reveals Abundant SNORD44-Derived Small RNAs

Small non-coding RNAs represent RNA species that are not translated to proteins, but which have diverse and broad functional activities in physiological and pathophysiological states. The knowledge of these small RNAs is rapidly expanding in part through the use of ...

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Hypoxic signature of microRNAs in glioblastoma: insights from small RNA deep sequencing

Hypoxic signature of microRNAs in glioblastoma: insights from small RNA deep sequencing

Hypoxia is a critical aspect of the glioma microenvironment and has been associated with poor prognosis and resistance to various therapies. However, the mechanisms responsible for hypoxic survival of glioma cells remain unclear. Recent studies strongly suggest that microRNAs act ...

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