Analysing transcriptomes: ACGT community receives hands-on training

A whole transcriptome sequencing (or RNA sequencing/RNA Seq) data analysis workshop was hosted for ACGT researchers from 15-19 May. The workshop was hosted by ACGT and facilitated by expert trainers from the University of Pretoria’s Centre for Bioinformatics and Computational Biology (CBCB, Prof Fourie Joubert) and the Agricultural Research Council’s Biotechnology Platform (Dr Charles Hefer and Dr Oliver Bezuidt).
RNA Seq aims to unravel the sum of all transcripts in an organism at any given moment in time and is a key intermediate step in the central dogma. The coverage of the technology is also still superior to technologies aiming to measure the full complement of proteins and metabolites in a living system, but at the same time further removed from the phenotype of an organism. Hence, transcriptome analysis can give important clues to changes occurring in an organism following a variety of environmental cues or life stage transitions.

The technology can be applied across multiple fields of study, and interest for the course was received from researchers and institutions with very different backgrounds and research aims. A total of 23 delegates could be accommodated for the week-long training event, hailing from the ARC (several different institutions), National Health Laboratory Service (NHLS), National Institute for Communicable Diseases (NICD), University of Pretoria (several medical, veterinary and agricultural delegates), as well as the University of the Witwatersrand.

The workshop included a mix of lectures and hands-on practical sessions in the CBCB training laboratory. Delegates were given a holistic view of all the aspects contributing to a successful transcriptome analysis, including coding in Linux, computing clusters as well as an introduction to next-generation sequencing (including experimental design, quality control and sequence alignment). A whole day was dedicated to analysing differential expression, and the last day was set aside for specific one-on-one sessions with delegates to address their specific queries or to clarify any issues that may have arisen.
Even though delegates were at very different levels in their experience with application of RNA Seq analysis, the feedback received following conclusion of the course was very positive. A possibility for future training events may be to split delegates into a beginners and advanced course, since interest in this specific course has always been high.

The ACGT would like to again thank the course facilitators for the immense effort and time invested in training partnership researchers.

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