Lecture slides


After a brief overview of the course, we’ll spend the opening lecture talking about Illumina’s ‘Sequencing by Synthesis’ technology, and walk through the steps involved in planning for a transcriptomics experiment. After this lecture, jargon like flow cell, single-end, paired-end, indexing, cluster density, library, ribo-depletion, scRNAseq, and fastq will pratically roll off your tongue.


  • Familiarity with Illumina’s ‘Sequencing by Synthesis’ (SBS) technology
  • Basics of setting up a sequencing experiment (read length vs depth, PE vs SE, etc.)
  • Understand data output from HTS


File formats produced by sequencing.

RNA-seqlopedia - Created by the Univ. of Orgeon, this is a great resource for understanding the entire RNAseq workflow.


Illumina’s SBS technology - Below is the video I showed in class. It’s a nice visual for how SBS works.