Lecture slides on iCloud

As the inaugural lecture for the course, we’ll spend this lecture discussing Illumina’s ‘Sequencing by Synthesis’ technology. We’ll also 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 practically roll off your tongue.

Learning objectives

  • Get familiar with jargon of RNAseq/HTS (paired-end, cluster density, fastq, index, etc)
  • Understand Illumina’s “Sequencing by Synthesis” (SBS) technology
  • Set priorities when planning a sequencing experiment
  • Understand the basics of library prep for 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.

Lecture videos

Part 1 - History of sequencing and details of Illumina’s ‘Sequencing by Synthesis’ (SBS) technology

Part 2 - Design considerations for RNAseq experiments, and the state-of-the-art for transcriptomics