We are more than excited to be part of this year’s virtual AGBT Meeting (March 1–3, 2021)!
Advances in Genome Biology and Technology meeting offers a unique experience where heads of labs, institutions, businesses, financial analysts, and other high-level stakeholders come together to advance the field and drive game-changing innovation. This event gives everyone the opportunity to announce and showcase new scientific advances and forge new partnerships.
This year we are presenting 3 posters, highlighting our newest products, that have recently been launched.
If you are attending the meeting, check our posters:
TraPR – The new gold standard in small RNA extraction for mature, physiologically relevant small RNAs across kingdoms
Dr. Yvonne Goepel
Product Manager, Lexogen
Regulatory small RNAs (sRNAs) play an essential role in mRNA turnover, translational regulation, and are thus important regulators of gene expression. These sRNAs associate with specific proteins of the Argonaute family (AGOs) to form RNA-induced silencing complexes (RISCs) and guide the AGO proteins to their respective targets in a process termed RNA interference.
Lexogen’s TraPR Small RNA Isolation Kit greatly facilitates the isolation of RISCs and associated small functional RNAs. It is based on TraPR (Trans-kingdom, rapid, affordable Purification of RISCs), a gel- and bias-free, column-based method (Grentzinger et al., 2020). Freshly harvested or flash frozen tissues, cells, or biofluids are lysed and loaded directly onto TraPR columns. While bulk RNA and DNA are retained on the column, only RISC-associated sRNAs are eluted. These steps are completed in 15 minutes, and the resulting RISC fraction can be analyzed directly, or further processed to extract sRNAs for targeted or global analyses, such as Northern Blot or small RNA sequencing (sRNA-Seq).
By purification of RISCs the TraPR Small RNA Isolation Kit enriches exclusively fully functional, physiologically relevant sRNAs including piRNAs, siRNAs, miRNAs, and scnRNAs. Contaminating RNAs such as degradation products of tRNA, rRNA, and mRNA are effectively excluded from the purified RISC fraction. TraPR is thereby superior to methods that are based on size-selection via columns or gel-purification and cannot distinguish between functional small RNAs and degradation products. Whereas other methods for functional sRNA isolation such as co-immunoprecipitation require intricate knowledge of the sample’s AGO composition, TraPR is universal and does not require prior characterization of the sample.
We show, in multiple benchmarking assays, that the TraPR kit considerably improves quality and consistency of sRNA sample preparation also from notoriously difficult-to-handle tissues/bio-fluids such as starchy storage roots or mammalian plasma and regardless of RNA contaminants or RNA degradation status of samples. TraPR works consistently over a large input range and eliminates the need for species-specific rRNA depletion.
In summary, the TraPR Small RNA Isolation Kit generates high-quality sRNA preparations suitable for Next Generation Sequencing (NGS) applications and thus provides a highly reproducible, time-saving method that outperforms all current gold-standard procedures for sRNA profiling. Small RNA isolation from liquid samples becomes easily accessible, making TraPR perfectly suited for biomarker discovery applications.
Grentzinger, Thomas; Oberlin, Stefan; Schott, Gregory; Handler, Dominik et al. (2020): A universal method for the rapid isolation of all known classes of functional silencing small RNAs. Nucleic Acids Research. DOI: 10.1093/nar/gkaa472.
QuantSeq-Pool sample-barcoded 3′ mRNA-Seq as cost-effective and scalable solution for transcriptome-wide gene expression profiling
Lukas Paul, PhD
Product Manager, Lexogen
Gene expression quantification by tag profiling has become a success story with now more than 600 publications citing the use of the Lexogen QuantSeq 3’ mRNA-Seq kit alone. The straightforward protocol generates RNA-Seq reads close to the poly(A) tails by oligo(dT) priming, reverse transcription and random-primed second strand synthesis. Data evaluation is robust and highly efficient, since reads mapped to the reference genome are simply counted without having to rely on complex transcriptome models. Only 2-5 M reads are needed to profile complex transcriptomes adding to the cost efficiency of the QuantSeq method, and already the standard kit is providing scalability from a few to hundreds of samples while maintaining quality control of individual samples by qPCR-guided library amplification settings and sample-specific library quantification.
QuantSeq-Pool, the latest addition to the QuantSeq family, is the optimal solution for gene expression profiling in large screening projects with homogeneous RNA input including FFPE samples. The protocol combines sample barcoding, early pooling, and batch processing of up to 96 samples in one single reaction. This results in a workflow that is ideal for projects of even the largest scale with triple barcoding providing up to 36,864 combinations of 12-nt indexes that are designed to minimize the impact of index sequence errors. The early pooling allows to prepare 96 samples manually or in automated setups in as little as 4.5 hours, and the approach also reduces technical variation in the complete workflow and saves up to ten times in sequencing and consumable costs. These features make QuantSeq-Pool a perfect choice to accelerate large-scale gene expression profiling projects.
LUTHOR – unparalleled sensitivity in single cell sequencing
Mantas Survila, PhD
Research Scientist, Lexogen
Cell-to-cell variability is a fundamental feature among multi-cellular organisms, which contain highly diverse cell types with unique transcriptome profiles. Sequencing of individual cells allows assessing heterogeneity in gene expression even between cells of similar type or origin. The requirement for thousands to millions of cells to compensate for inefficient library conversion limits the usability of these methods for cells that are notoriously hard to isolate in large quantities, and for studying perturbations on a cell-to-cell level.
LUTHOR 3’ mRNA-Seq uses Lexogen’s proprietary THOR Amplification Technology to enable high-resolution sequencing of single cells with unprecedented sensitivity. RNA is amplified directly from the original mRNA molecules eliminating the need for amplification of cDNA intermediates. The protocol enables 3’ mRNA-Seq even from challenging ultra-low input samples, or individual cells that are notoriously difficult to handle. LUTHOR outperforms all conventional single-cell RNA-Seq methods which detect only highly abundant genes and require extremely large numbers of cells. Thereby, LUTHOR enables in-depth analysis of cellular transcriptomes and unlocks the full potential of single-cell sequencing by allowing to assess gene expression changes even for medium and low abundant transcripts in individual cells. The combination of the innovative RNA Amplification and the highly efficient library generation technologies offers unprecedented sensitivity for ultra-low input and single cells, with up to ~15,000 genes detected from one single cell at 1 M reads (CPM >1).