Adiconis and co. published an analysis in Nature Methods showing that CAGE is the best method for 5'-end RNA-#sequencing. It is a nice benchmark with overall a strong design.
Our #nanoCAGE method was also tested and performed poorly in the hands of the authors. However, they used 7.5 μg of total #RNA as starting material, which is totally out of the range that we designed nanoCAGE for. Therefore, I have posted a response on #PubPeer explaining that fact.
When BLT is about beads and transposases and not bacon and tomatoes Show more
The #Nextera DNA Flex kits use bead-bound #Tn5 transposase to 1) standardise the size range of the #sequencing libraries and 2) standardise the amount yielded by the reaction (which is a crucial step before loading the #Illumina DNA sequencers). I had completely overlooked it for quite some time. I did not try it, but the idea is smart. I have not looked at the price either...
Needing a new laptop at work that can run #Microsoft Office, I was tempted to try again #Windows after more than a decade on OSX, because I am quite curious about the windows #subsystem for Linux. Unfortunately, the laptop that I wanted to buy was only available in Japanese, and despite we are in 2018 it seems that MS still sells "single-language pack" systems were English can not be installed. Thus, I am going for a Mac instead. And of course running #Linux on my main desktop. Sorry MS, you must do better!
Poster flash talks in conferences: nice idea, but it takes precious time, so I was unsure if it was worth doing it, but recently I realised that it is an excellent opportunity to show videos, which obviously can not be on the posters (at least for the moment...).
Ranting on #PubPeer about authors who did not seem to check that their introduction was still up to date before submitting their paper: https://pubpeer.com/publications/4EDEA0037B3F02198380AC1A5B3543
High-throughput homologous recombination mutagenesis in yeast with libraries of plasmids providing the DNA template for recombination and expressing a guide RNA for inducing the recombination with a CRISPR-Cas9 break: 3 papers in last week's issue of Nature Biotechnology. https://www.nature.com/nbt/volumes/36/issues/6
Transparency on scientific instruments Show more
Manuscripts co-authored by instrument makers are less trused by the readers, according to a poll of a thousand researchers made by Carsten Bergenholtz, Samuel C MacAulay, Christos Kolympiris and Inge Seim.
Since this is an incentive to hide the participation of companies to research projects, they then argue that receiving discounts on instruments in that context should be listed as potential conflict of interest.
Published in "EMBO reports": http://embor.embopress.org/content/19/6/e45853
"Preproducibility", a new word to foster reproducible research. Show more
In his commentary "Before reproducibility must come preproducibility" published in Nature this week, Philip B. Starck invents a new word to urge researchers to provide detailed instructions on how to repeat experiments. https://doi.org/10.1038/d41586-018-05256-0
This is very much in line with the "registered reports" concept fostered by BMC and other publishers. It should be an essential part of research planning.
With long-lasting human biological materials, such as stem cells, initial donor #consent is necessary but not sufficient, write Boers & Bredenoord in Nature Cell Biology. https://www.nature.com/articles/s41556-018-0112-5
The authors underline that donors need to be informed about the future governance of the biomedical projects to which they contribute. This in line with the initiative to create a code of #conduct for health research in the wake of EU's General Data Protection Regulation (#GDPR). http://code-of-conduct-for-health-research.eu/
Now I am fully convinced that the 5′ #RNA cap is reverse-transcribed. Show more
All the pieces of the puzzle fit together. An extra G is found at the 5′ end of cDNAs. The reverse-transcriptase can add extra nucleotides to blunt DNA/RNA duplexes. Addition of nucleotide monophosphates in the reaction enhances the addition of the complementary nucleotides to the cDNA. 5′ -5′ GpppG can hybridise to a CpC overhang of a RNA duplex. The cap probably can enter the active site in a similar manner. http://charles.plessy.org/tags/reverse_transcription/
I will be moving to #OIST (Okinawa Institute of Science and Technology) on August 1st, to join the Luscombe laboratory (Genomics and Regulatory Systems Unit). Expect more posts on marine creatures, although my core activities will still revolve around nucleic acids, genetic programs and free software.
The article also states: "Use of a software product incorporating such open source license requirements in a medical device may increase the risk that the medical device is disapproved by regulatory bodies due to being tamper-prone or otherwise unsafe."
Is that #FUD or did that happen at least once in the past ?
Bio-IT World published an article entitled "Open Source Pitfalls At The Biotechnology-High Technology Crossover" by Paul Liu (May 14, 2018) http://www.bio-itworld.com/2018/05/14/open-source-pitfalls-at-the-biotechnology-high-technology-crossover.aspx
In very brief, it reminds to people new to the field that open source softwares have licenses that vary in what they permit, and that one needs to be careful when combining software with different licenses. Key recommendations: monitoring, documentation, anticipation.
Major update of the CAGEr package for bioinformatics analysis of transcription start sites. Show more
Main improvements are memory efficiency, speed and parallelism, but I also added some new plot functions for quality controls.
The theme is "Open Science's Impact on Research Careers". https://euraxess.ec.europa.eu/worldwide/japan/european-research-day/european-research-nights-2018
Interesting... when replying to content-warning (CW) posts, the CW is sticky and has to be removed manually.