siTOOLs Biotech Blog

A journey into the gut microbial control center: small RNA’s influence on Bacteroides thetaiotaomicron’s metabolism

26. May 2023 Laura Leiva Comments 0 Comment

Bacteroides thetaiotaomicron is a commensal bacterium that inhabits primarily the human large intestine and is considered one of the most important members of this microbial community. B. thetaiotaomicron is a highly versatile microbe, capable of utilizing a wide range of carbohydrates including those that are indigestible by human enzymes. It breaks down complex polysaccharides from plant cell walls and other dietary sources, producing short-chain fatty acids (SCFAs) that are an important energy source for humans. Furthermore, it has also been Read More

The Hidden World of Microbiomes and Their Impact on Our Lives

10. May 2023 Laura Leiva Comments 0 Comment

Microbiomes are the diverse communities of microorganisms that inhabit different parts of our bodies, as well as the environment around us. In recent years, research has revealed the vast and complex hidden world of microbiomes and their impact on our lives, from influencing our digestion and immune system to potentially affecting our mood and behavior. Advances in technology have enabled scientists to study microbiomes in unprecedented detail, leading to new insights into their diversity and functions. Understanding the microbiome and Read More

Microbiome May Blog Series

8. May 2023 Laura Leiva Comments 0 Comment

Hi there and welcome to our May blog series inspired by microbiomes🧫👾! We’re excited to announce that we will be launching a new blog series on microbiomes, featuring topics ranging from human microbiomes to marine sponges’ microbiomes. Our riboPOOLs kits have been used in numerous studies exploring the intricacies of microbiomes, and we’re thrilled to share our knowledge with you. Additionally, as May is the month of microbiomes, we are offering a 15% discount on all of our microorganism riboPOOLs kits and probes (24 and 96 reactions). Read More

Similar seed effects in independent siRNA screens

3. May 2023 Andrew Walsh Comments 0 Comment

A 2013 study on Parkin translocation used genome-wide siRNA libraries from Ambion (single Silencer Select siRNAs) and Dharmacon (pools of 4 siGENOME siRNAs). The correlation between results for the same on-target gene from the two libraries was very low (R = 0.09). (Each point in the following plot is for a gene.) The correlation between results for the same 7mer seed were higher (0.26), providing another example of the Iron Law of RNAi Screening. (Each point in the following plot Read More

A Brief Interview with Dr. Blaine Fritz

3. November 2022 Laura Leiva Comments 0 Comment

Chronic diseases like lower extremity wounds, which prevail in diabetic patients, are expensive to treat and cause reoccurring trauma to patients. Diabetic-related foot ulcers (DFUs) are also highly prone to infections, which increases the risk of hospital admission and amputation. Therefore, properly classifying infection severity in lower extremity ulcers is essential to guide appropriate treatment. Presently, clinicians and researchers use subjective classification systems to stratify lower extremity ulcer infections for treatment and research. These classifications are based on guidelines that Read More

The Iron Law of RNAi Screening

6. September 2022 Andrew Walsh Comments 0 Comment

This is the lead singer of a band called Iron Law. He looks like a researcher experiencing massive frustration after discovering what we call the Iron Law of RNAi Screening. This law states that in any screen with low-complexity reagents (single siRNAs like Silencer Selects, or mini-pools like Dharmacon SMARTpools), off-target effects will predominate. Given that the average lone siRNA will down-regulate nearly 100 off-target genes, but has only a single on-target gene, it is not hard to see how Read More

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