RNA sequencing

RNA sequencing

RNA sequencing techniques are used to determine the sequence of nucleotide bases, adenine (A), cytosine (C), guanine (G) and uracil (U) in RNA molecules.

Usually RNA is first converted into cDNA (complementary DNA) with a reverse transcriptase enzyme and then a second strand synthesis reaction is performed so that DNA sequencing techniques can be applied to double stranded DNA copies of RNA transcripts. Since this method can lose information from the 5' and 3' ends of the transcript, other methods have been developed that omit the second strand synthesis reaction and ligate adapters to the cDNA for sequencing reactions. Sequencing adapters are consistent sequences that when applied to flank the cDNA fragments produces a cDNA library.

RNA sequencing is replacing gene expression arrays to analyse the spectrum and abundance of transcripts in a given cell or tissue type at a given time. The technique called RNA-Seq, also known as whole transcriptome shotgun sequencing generates cDNA and uses it in next-generation sequencing.

UK-based Oxford Nanopore Technologies devised a system to directly sequence RNA with a device called the MinION, where electrical current is applied across a nanoscale molecular pore and current fluctuations detect the RNA sequence as the RNA molecule snakes through the pore. This RNA sequencing device was used by NASA on the International Space Station because NASA is interested in using it to identify on board microorganisms and to monitor changes in human health or microbiomes and also the possibility of detecting life based on DNA or RNA elsewhere in the universe.

RNA-Seq delivers an unbiased and unprecedented high-resolution view of the global transcriptional landscape, which allows an affordable and accurate approach for gene expression quantification and differential gene expression analysis between multiple groups of samples. RNA-Seq can identify novel and previously-unexpected transcripts without the need for a reference genome, allowing de novo assembly of new transcriptome that is not previously studied before. It also enables the discovery of novel gene structures, alternatively spliced isoforms, gene fusions, SNPs/InDel, and allele-specific expression (ASE).

i. RNA-Seq is a sensitive tool for gene expression profiling. Compared to microarray, RNA-Seq offers a digital read that is more accurate for all gene expression.

The authors found 1089 genes differentially expressed between the CLL and normal B cells (Table 1). As was expected, the most differentially expressed genes are immunoglobulins due to the clonality of the CLL cells. Pathway analyses revealed that genes involved in metabolic pathways had higher expression in CLL, while genes related to splicesome, proteasome, and ribosome were substantially down-regulated in CLL.

Figure 1. CLL transcriptional landscape. (A) The coding potential of differentially expressed genes between the CLL and normal samples. (B) Normalized expression of transposable elements (TEs). (C) Genes with condition-specific splicing ratios. (D) Allele-specific expression of somatic mutations.

Figure 4. Major transcriptional CLL subgroups. (A) Clustering of CLL and normal samples. (B) Consensus cluster. (C) Multidimensional scaling of CLL and normal samples based on gene expression. (D&E) Enrichment score plot.

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Research and Markets
December 21, 2020
www.prnewswire.com:443
/PRNewswire/ -- The "The Market for RNA Sequencing" report has been added to ResearchAndMarkets.com's offering. The sequencing market has continued to provide...
Science X staff
December 21, 2020
phys.org
We've all suffered from viruses, but did you know that they are also a problem for mushrooms and molds? Mycoviruses are viruses that specifically infect fungi and have the potential to impact ecology, agriculture, food security, and public health. Understanding the nature of these viruses, including their number and evolution, can help us understand their origins and inform our understanding of viruses in general.
Research and Markets
November 26, 2020
www.prnewswire.com:443
/PRNewswire/ -- The "RNA Analysis/Transcriptomics Market by Product (Reagents, Instruments, Software), Technology (Microarrays, NGS, Sanger), Application...
Zhang Nannan
November 23, 2020
phys.org
After double fertilization, zygotic activation occurs that initiates a new life cycle, followed by cell divisions, cell differentiation and organogenesis. During post-embryonic development, stem cells located in shoot apical meristem (SAM) and root apical meristem (RAM) allow plants to continuously generate new tissues and organs. Therefore, understanding the role of zygote activation and stem cell homeostasis is a long-standing interest to scientists.
Science X staff
November 18, 2020
phys.org
Organ and stem cell transplants are proven and frequently used methods in modern clinical practice. However, even when performed regularly in specialized centers, some patients still experience a number of serious complications afterwards. Among other things, infections with fungi and viruses can jeopardize therapeutic success. For example, coinfection with cytomegalovirus, which belongs to the family of Herpes viruses, and the fungus Aspergillus fumigatus can be critical. This combination of pathogens poses a serious medical threat in organ and stem cell transplantation.
November 17, 2020
BioSpace
NantHealth and ImmunityBio Announce RNA Profiling for Clinical Decision Support Publication In Nature's Scientific Reports - read this article along with other careers information, tips and advice on BioSpace
Hospital for Special Surgery
November 8, 2020
www.prnewswire.com:443
/PRNewswire/ -- Since doctors began treating cancer patients with immunotherapy drugs called checkpoint inhibitors nearly a decade ago, they have observed that...
Esther Landhuis
July 28, 2020
Scientific American
Scientific American is the essential guide to the most awe-inspiring advances in science and technology, explaining how they change our understanding of the world and shape our lives.

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