20.109(S18):Analyze RNA-seq data and prepare for quantitative PCR experiment (Day 4)

Introduction

Protocols

Part 1: Analyze RNA-seq data

Today you will analyze the RNA-seq data gathered from untreated DLD-1 and BRCA2- cells and etoposide treated DLD-1 and BRCA2- cells. Following RNA purification, the samples were submitted to the BioMicro Center for Illumina sequencing. Illumina sequencing technology, or sequencing by synthesis (SBS), is used for massively parallel sequencing with a proprietary method that detects single bases as they are incorporated into growing DNA strands.

Analysis of RNA-Seq data by Amanda Kedaigle, Prof. Ernest Fraenkel & Prof. Leona Samson.

Part 2: Design primers for qPCR

Navigation links

Next day: Investigate RNA-seq data using public databases

Previous day: Purify RNA and practice RNA-seq data analysis methods