siTOOLs Biotech Blog

The creation of the siFractor- an interview with Dr. Jan Medenbach

9. August 2022 Laura Leiva Comments 0 Comment

siTOOLs latest device, the siFractor is a game changer for any application involving the fractionation of centrifugated samples. Its applications include isolation of protein complexes and RNPs, purification of extracellular vesicles and ribosome profiling (Ribo-Seq). We sat with the co-creator of the siFractor, Dr. Jan Medenbach and asked him how the siFractor works, its benefits and what led him to co-create this device. Could you tell us briefly about yourself My name is Jan Medenbach. I’m a Group Leader at Read More

siTOOLs Biotech sponsors Argonautes Conference 2022

13. July 2022 Laura Leiva Comments 0 Comment

MUNICH, GERMANY – siTOOLs Biotech GmbH, a young, research-driven biotech company based in Munich/Martinsried and rapidly growing in the field of functional genomics and Next-Generation RNA sequencing, today announced its support for the upcoming Argonautes Conference 2022 at University of Regensburg as lead sponsor. The conference, organized by Prof. Gunter Meister from University of Regensburg, and Prof. Martin Simard of CHU de Québec-Université Laval Research Center, will be held from 24th to 27th August 2022. The conference’s scientific program will Read More

A brief interview with Dr. Mar Martinez Pastor

1. June 2022 Laura Leiva Comments 0 Comment

Dr. Mar Martinez Pastor is a microbiologist from Valencia, who currently works as a senior Research Scientist in the Schmid Lab (leader Dr. Amy Schmid) at Duke University. She is a specialist in microbial response to abiotic stress. At the Schmid lab her research is focused on the transcriptional regulation of iron homeostasis in halophilic archaea. Halophilic archaea are salt-loving archaea, which can be found in hypersaline environments like the colorful salt pond pictured above in San Francisco Bay, California. Read More

An artist’s rendition of a ribosome. Credit: C. BICKLE/SCIENCE

Ribo-depletion in RNA-Seq – Which ribosomal RNA depletion method works best?

12. August 2019 Catherine Goh Comments 0 Comment

Summary: This blogpost is focussed on ribosomal RNA (rRNA) depletion methods frequently applied to improve and economize RNA-Seq experiments. The Rise of RNA-Seq RNA-Seq Overtakes Microarrays The use of Next-Generation RNA Sequencing (RNA-Seq) has recently overtaken that of DNA-based microarrays to detect and quantify changes in gene expression. Why? RNA-Seq can detect novel coding and non-coding genes, splice isoforms, single nucleotide variants and gene fusions. Its broader dynamic range also enables sensitive detection of low abundance transcripts. Also, technological advancements in Read More

Low hit validation rate for Dharmacon siGENOME screens

4. September 2018 Andrew Walsh Comments 0 Comment

Good experimental design is important when validating hits from RNAi screens. Off-target effects from single siRNAs and low-complexity siRNA pools (e.g. Dharmacon siGENOME) result in high false-positive rates that must be sorted out in validation experiments. Dharmacon siGENOME pools (SMARTpools) have 4 siRNAs, and the most common form of validation is to test the pool siRNAs individually (deconvolution). Unfortunately, the results of such deconvolution screening rounds are difficult to interpret. The pool phenotype could be due to the off-target effects of Read More

Clearly compensating

27. August 2018 Andrew Walsh Comments 0 Comment

Genetic compensation by transcriptional adaptation is a process whereby knocking out a gene (e.g by CRISPR or TALEN) results in the deregulation of genes that make up for the loss of gene function. A 2015 study by Rossi et al. (discussed previously) alerted researchers that CRISPR/TALEN knock-out experiments may be subject to such effects. Genetic adaption or compensation had been well known to mouse researchers creating knock-out lines. In fact, one of our company founders also ran into this when trying to confirm Read More

Pooling only 4 siRNAs increases off-target effects

20. August 2018 Andrew Walsh Comments 0 Comment

In a previous post, we showed how siRNA pools with small numbers of siRNAs can exacerbate off-target effects. Low-complexity pools (with 4 siRNAs per gene) should thus lead to overall stronger off-target effects than single siRNAs. This phenomenon was addressed in a bioinformatics paper a few years back. The authors created a model to predict gene phenotypes based on the combined on-target and off-target effects of siRNAs. The siRNAs were screened either individually (Ambion and Qiagen), or in pools of four Read More

Citations of our Nucleic Acids Research Paper

14. August 2018 Andrew Walsh Comments 0 Comment

Our 2014 Nucleic Acids Research paper provides an excellent overview of the siPOOL technology. Google Scholar shows that our paper has been cited 64 times. To put this into perspective, the 2012 PLoS One paper on C911 controls by Buehler et al. has 72 citations. C911 controls are probably the most effective way to determine whether a single-siRNA phenotype is due to an off-target effect. These citation numbers show that siPOOLs have good mind share when researchers consider the issue of Read More

Performing target validation well

24. July 2018 Catherine Goh Comments 0 Comment

Summary This blogpost describes issues encountered in target validation and how to safeguard against poor reproducibility in RNAi experiments. The importance of target validation More than half of all clinical trials fail from a lack of drug efficacy. One of the major reasons for this is inadequate target validation. Target validation involves verifying whether a target (protein/nucleic acid) merits the development of a drug (small molecule/biologic) for therapeutic application. Failing to adequately validate a target can burden a pharma with roughly 800 million to 1.4 billion in Read More

Low complexity pooling does not prevent siRNA off-targets

17. April 2018 Andrew Walsh Comments 0 Comment

Summary: Low-complexity siRNA pooling (e.g. Dharmacon siGENOME SMARTpools) does not prevent siRNA off-targets. It may in fact exacerbate off-target effects. Only high-complexity pooling (siPOOLs) can reliably ensure on-target phenotypes. Low-complexity pooling increases the number of siRNA off-targets One of the claims often made in favour of low-complexity pooling (e.g Dharmacon siGENOME SMARTpools) is that this pooling reduces the number of seed-based off-target effects compared to single siRNAs. If this were true, we would expect different low-complexity siRNA pools for the same Read More