Lecture slides on iCloud

Homework #1: DataCamp Intro to R course (~2hrs) - due 3pm next Wednesday, April 22nd.


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 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
  • Have a sense for how single cell sequencing (scRNAseq) and spatial transcriptomics fit into the evolving landscape of transcriptomics


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 video

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