Microbial Genetics
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Are journals ready to abolish peer review?

Are journals ready to abolish peer review? | Microbial Genetics | Scoop.it
Scientific journal publishing has undergone significant changes in the last couple of decades with the digital revolution and the rise of open access journals. However, the process of manuscript peer review remains essentially the same as it was in the age of typewriters, even if we now do it by email rather than by post. Typically two or three copies of the manuscript are sent to two or three referees, and the decision to publish is based on their reports. Is this system quaint and outdated in today’s world of instant communication, social media and crowdsourcing? Or has it prevailed because it actually works?
John Bohannon’s sting published in Science, the rise in retractions and disillusionment with the ...Read more
Andres Sebastian Espindola's insight:

In this case, when using peer-reviewers we are asking the neighbor next door that is growing the same crop we are growing; to let us sell our product before his product.  You tell me if this works.

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Scooped by Andres Sebastian Espindola
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Whole-transcriptome RNAseq analysis from minute amount of total RNA

Whole-transcriptome RNAseq analysis from minute amount of total RNA | Microbial Genetics | Scoop.it
Andres Sebastian Espindola's insight:

RNA sequencing approaches to transcriptome analysis require a large amount of input total RNA to yield sufficient mRNA using either poly-A selection or depletion of rRNA. This feature makes it difficult to miniaturize transcriptome analysis for greater efficiency. To address this challenge, we devised and validated a simple procedure for the preparation of whole-transcriptome cDNA libraries from a minute amount (500 pg) of total RNA. We compared a single-sample library prepared by this Ovation RNA-Seq system with two available methods of mRNA enrichment (TruSeq poly-A enrichment and RiboMinus rRNA depletion). Using the Ovation preparation method for a set of eight mouse tissue samples, the RNA sequencing data obtained from two different next-generation sequencing platforms (SOLiD and Illumina Genome Analyzer IIx) yielded negligible rRNA reads (<3.5%) while retaining transcriptome sequencing fidelity. We further validated the Ovation amplification technique by examining the resulting library complexity, reproducibility, evenness of transcript coverage, 5' and 3' bias and platform-specific biases. Notably, in this side-by-side comparison, SOLiD sequencing chemistry is biased toward higher GC content of transcriptome and Illumina Genome analyzer IIx is biased away from neutral to lower GC content of the transcriptomics regions.


Andres says: It's not only about total RNA integrity.  It's all about mRNA integrity and mRNA representation.... 

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