SLAMdunk – Another Optimized Lexogen, BlueBee Pipeline to Simplify Data Analysis

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In September this year, Lexogen released the family of SLAMseq Metabolic RNA labeling kits, the underlying methodology of which is based on S4U labeling of RNA in cell cultures, alkylation of RNA with iodoacetamide, and the consequent introduction of T to C mutations in cDNA.

To simplify the data analysis component for users of the SLAMseq labeling kit, Lexogen together with BlueBee integrated the analysis pipeline SLAMdunk - developed by scientists from the IMP, MFPL, and IMBA research institutes in Vienna, Austria - onto the BlueBee platform. This new integration allows Lexogen SLAMseq kit users to run the data analysis via a simplified user interface on the secure and optimized, BlueBee cloud-based platform. Best of all, analysis with the SLAMdunk is included with all SLAMseq kits to simplify the entire analysis process.

The SLAMseq Metabolic RNA labeling kits were previously described in two papers by Herzog et al., 2017. SLAMseq (Thiol (SH)-Linked Alkylation for the Metabolic sequencing of RNA) enables the identification and quantification of newly synthesized (nascent) and existing RNA from the same sample in parallel, without the need for biochemical isolation. SLAMseq can be readily applied to living cell experiments. Combined with QuantSeq 3’ mRNA-Seq library preparation, SLAMseq provides a high-throughput solution for analyzing transcriptome-wide RNA synthesis and turnover kinetics.

The SLAMdunk pipeline consists of five major analysis steps:

  1. map step: All reads are aligned to a reference genome
  2. filter step: Retains unique alignments satisfying certain quality criteria
  3. snp step: Variants are called and excluded from further analysis
  4. count step: The T to C conversion rate and the ratio of nascent RNA is determined
  5. alleyoop step: Produces summary statistics, a PCA (Principle Component analysis) for all samples, and several conversion rate plots (read based, UTR based, read position based)

We are excited that with the BlueBee platform we can deliver optimized and simplified data analysis for complex pipelines in a secure environment, thus helping researchers getting to their insights faster.

This collaboration with Lexogen follows the QuantSeq 3’mRNA-Seq analysis pipeline which was released in 2016. Learn more about the Lexogen - BlueBee RNA-seq analysis solution from a recent interview with Dr. Dalia Daujotyte (Head of Business Development at Lexogen) discussing the need for end-to-end RNA-seq solutions and the relevance of the partnership with BlueBee.

Find out more about the data analysis for QuantSeq and SLAMseq.