“In collaboration with Bluebee we already offer complimentary data analysis to all QuantSeq 3’mRNA-Seq users thus providing full workflow to ensure highest quality results from the RNA-Seq experiment. Now all SLAMseq users will also have access to a secure, user-friendly and well-defined data analysis on Bluebee platform. “ – Dalia Daujotyte, Head of Business Development at Lexogen.
The family of SLAMseq Metabolic RNA labeling kits was successfully released in September this year accompanying the publication of the SLAMseq application in the Nature Methods journal. The method is based on S4U labeling of RNA in cell cultures, alkylation of RNA with iodoacetamide, and consequent introduction of T to C mutations in cDNA. By just adding two extra steps to RNA-Seq workflows, the SLAMseq approach provides a unique tool for the study of RNA metabolism. Synthesis and degradation can be monitored transcriptome-wide by analyzing nascent and steady-state RNA levels in the same cell extract.
“At Bluebee we are helping to drive research in gene expression, not only by providing standardized execution and reducing the data analysis burden but by helping people get more knowledge and insights from their genomic data.“ said Hans Cobben, CEO of Bluebee.
The SLAMdunk pipeline consists of 5 major steps. In the map step reads are aligned to a reference genome, and in the filter step unique alignments satisfying certain quality criteria are retained. In the snp step variants are called and excluded from further analysis. In the count step, the T to C conversion rate and the ratio of nascent RNA is determined. The alleyoop step then produces summary statistics, a Page 2 of 2 Public PCA for all samples, and several conversion rate plots (read based, UTR based, read position based).
Lexogen is a transcriptomics and next generation sequencing company, focusing on the development of technologies for complete transcriptome sequencing. Its portfolio includes innovative molecular biology kits, software, and services for RNA-Seq. To learn more, visit www.lexogen.com and follow @lexogen
Contact Bluebee @Karen Frost