A comparison between whole transcript and 3' RNA sequencing methods using Kapa and Lexogen library preparation methods.

Background3' RNA sequencing provides an alternative to whole transcript analysis. However, we do not know a priori the relative advantage of each method. Thus, a comprehensive comparison between the whole transcript and the 3' method is needed to determine their relative merits. To this end, we used two commercially available library preparation kits, the KAPA Stranded mRNA-Seq kit (traditional method) and the Lexogen QuantSeq 3' mRNA-Seq kit (3' method), to prepare libraries from mouse liver RNA. We then sequenced and analyzed the libraries to determine the advantages and disadvantages of these two approaches.ResultsWe found that the traditional whole transcript method and the 3' RNA-Seq method had similar levels of reproducibility. As expected, the whole transcript method assigned more reads to longer transcripts, while the 3' method assigned roughly equal numbers of reads to transcripts regardless of their lengths. We found that the 3' RNA-Seq method detected more short transcripts than the whole transcript method. With regard to differential expression analysis, we found that the whole transcript method detected more differentially expressed genes, regardless of the level of sequencing depth.ConclusionsThe 3' RNA-Seq method was better able to detect short transcripts, while the whole transcript RNA-Seq was able to detect more differentially expressed genes. Thus, both approaches have relative advantages and should be selected based on the goals of the experiment

Identification of new SOX2OT transcript variants highly expressed in human cancer cell lines and down regulated in stem cell differentiation

Long non-coding RNAs are manifested as a new paradigm of molecular effectors in a wide range of human diseases. Human SOX2 overlapping transcript (SOX2OT) gene can generate six lncRNA transcript variants which are functionally assumed to be correlated with cellular differentiation and carcinogenesis. However, the circumstances determining expressional and functional differences between SOX2OT transcript variants remain to be explored. Here, we studied the expression of all SOX2OT transcript variants specifically in five human cancer cell lines by real-time RT-PCR. Changes of the new SOX2OT transcript variants expression were measured during the NT2 teratocarcinoma cell line neuronal-like differentiation and were compared to pluripotency regulators, SOX2 and OCT4A gene expressions. Surprisingly, we identified two new SOX2OT transcripts, named SOX2OT-7, SOX2OT-8 which lack exon 8. We discovered that beside active proximal and distal SOX2OT promoters, different cancer cell lines express high levels of some SOX2OT transcript variants differentially by alternative splicing. Significantly, both SOX2OT-7 and SOX2OT-8 are highly expressed in human cancer cell lines coinciding with SOX2, one of the pluripotency regulators. Our results revealed that SOX2OT-7 is almost the most abundant form of SOX2OT transcript variants in the examined cancer cell lines particularly in NT2 teratocarcinoma cell line where its expression falls upon neuronal-like differentiation similar to SOX2 and OCT4A. We suggest that at least some of SOX2OT transcripts are significantly associated with cancer and stem cell related pathways. © 2015, Springer Science+Business Media Dordrecht

Identification of an Alternative Exon in a GABA Receptor Gene

The central dogma of biology states that DNA is transcribed into mRNA, which is then translated into proteins. In order for translation to occur, pre-mRNAs first must be processed. In pre-mRNA processing, parts of the nucleotide sequence called introns are spliced out from the transcript, so the final mRNA is made up entirely of exons. In alternative splicing, an exon is spliced out of the pre-mRNA transcript much like an intron. An mRNA transcript produced as a result of alternative splicing could produce a different protein than the mRNA without alternative splicing. Alternative splicing of an mRNA transcript could also result in a premature termination codon (PTC) within the mRNA sequence. This premature termination codon causes translation to stop before the full transcript has been translated, resulting in a truncated protein. Nonsense Mediated Decay (NMD) functions by degrading mRNA transcripts containing a PTC. NMD occurs during translation by an intricate series of protein-protein and protein-mRNA interactions that detect a PTC and result in the cleavage of PTC-containing mRNAs. We discovered an alternative exon in a zebrafish GABA receptor gene that leads to a PTC when excluded from the final mRNA and investigated the role of NMD in degrading the PTC-containing transcript

Transcript of Battle Stations

This story is an excerpt from a longer interview that was collected as part of the Launching through the Surf: The Dory Fleet of Pacific City project. In this story, Mike Cellers recounts stories of finding schools of silvers and his friend Windy Wenzinger catching a big Chinook salmon

Making a Killing: Science Fiction Through the Lens of Nordic Noir in 'Crocodile' and 'Hated in the Nation'

Crime stories originating from Northern Europe have enjoyed critical and, to varying degrees, commercial success in the fields of cinema, television and literature, spawning translations, adaptations, and even international imitations paying visible homage to the distinctive aesthetic and thematic characteristics of the form, which have become so recognisable they have evolved into a generic type of their own – ‘Nordic Noir’. In this article, Dan Ward examines Black Mirror's conspicuous mobilisation of the conventions of Nordic Noir in two distinctive episodes. Drawing on a range of critical perspectives and noteworthy examples of the genre, Ward investigates the repurposing of Scandinavian crime fiction's familiar social critique to contemporary concerns around creeping surveillance and the rise of corporate technocracy in neoliberal democracies

History of British Intensive Care, c. 1950–c. 2000

Annotated and edited transcript of a Witness Seminar held on 16 June 2010. Introduction by Professor Sir Ian Gilmore, Royal Liverpool Hospital and University of Liverpool.Annotated and edited transcript of a Witness Seminar held on 16 June 2010. Introduction by Professor Sir Ian Gilmore, Royal Liverpool Hospital and University of Liverpool.Annotated and edited transcript of a Witness Seminar held on 16 June 2010. Introduction by Professor Sir Ian Gilmore, Royal Liverpool Hospital and University of Liverpool.Annotated and edited transcript of a Witness Seminar held on 16 June 2010. Introduction by Professor Sir Ian Gilmore, Royal Liverpool Hospital and University of Liverpool.Annotated and edited transcript of a Witness Seminar held on 16 June 2010. Introduction by Professor Sir Ian Gilmore, Royal Liverpool Hospital and University of Liverpool.Annotated and edited transcript of a Witness Seminar held on 16 June 2010. Introduction by Professor Sir Ian Gilmore, Royal Liverpool Hospital and University of Liverpool.Annotated and edited transcript of a Witness Seminar held on 16 June 2010. Introduction by Professor Sir Ian Gilmore, Royal Liverpool Hospital and University of Liverpool.Annotated and edited transcript of a Witness Seminar held on 16 June 2010. Introduction by Professor Sir Ian Gilmore, Royal Liverpool Hospital and University of Liverpool.Intensive care developed in the UK as a medical specialty as the result of some extraordinary circumstances and the involvement of some extraordinary people. In 1952, the polio epidemic in Copenhagen demonstrated that tracheostomy with intermittent positive pressure ventilation saved lives and those infected with tetanus (common in agricultural areas) soon benefited. War-time developments such as triage, monitoring, transfusion and teamwork, and different specialists such as respiratory physiologists, anaesthetists and manufacturers of respiratory equipment all improved emergency treatment. These advances were rapidly extended to the care of post-operative patients, particularly with developments in cardiac surgery. Dedicated units appeared in the early 1960s in Cambridge, London and Liverpool, and later specialist care units were created for prenatal, cardiac and dialysis patients. The importance of specialist nursing care led to the development of nurse training, education and the eventual appointment of nurse consultants in the NHS in 1999. The specialty of intensive care was granted Faculty status by the GMC in 2010. Introduced by Professor Sir Ian Gilmore, this transcript includes, inter alia, the development of cardiac catheters, monitoring equipment, data collection techniques and the rise of multidisciplinarity, national audit, and scoring systems