Dataset summaries

For the tutorials we have set up multiple data sets:

A431 cell line RNA-Seq data

In most of the exercises, we will use RNA-Seq data from the A431 cell line. It is an epidermoid carcinoma cell line which is often used to study cancer and the cell cycle, and as a sort of positive control of epidermal growth factor receptor (EGFR) expression. A431 cells express very high levels of EGFR, in contrast to normal human fibroblasts.

The RNA-Seq data that we are going to use are from an experiment where the A431 cells were treated with gefinitib, which is an EGFR inhibitor and is used (under the trade name Iressa) as a drug to treat cancers with mutated and overactive EGFR. In the experiment, RNA was extracted at four time points: before the gefinitib treatment (t=0), and two, six and twenty-four hours after treatment (t=2, t=6, t=24, respectively), and sequenced using an Illumina HiSeq instrument in triplicates (thus there are 3x4=12 samples).

This data set or parts of it will be used in the labs on read mapping, transcript assembly, visualization, quality control and differential expression. There are many relevant questions that could be asked based on these measurements. In the QC exercise we are going to examine if the RNA libraries that we work with are what we think they are or if there are some missannotations on the datasets. In the isoform exercises we are going to look at some specific regions where the mass-spectrometry data indicated that novel exons or splice variants could be present at the protein level. We will use (part of) the RNA-Seq data to examine if there is corresponding evidence on the mRNA level, and how different software tools could be used to detect novel gene variants.

sRNA dataset

This dataset contains a few small RNA libraries, from Drosophila melanogaster (fruit fly) embryos and two cell lines (KC167 cells derived from whole embryos, and ML-DmD32 cells derived from adult wing discs). This is a subset of a much larger data set used to study microRNAs and other small RNAs in Drosophila. These data sets are described more in this paper.

Long reads

This data set contains three PacBio reads for the gene RAB11FIP5, extracted from a full-length RNA sequencing data set released by PacBio in 2014. For more info go here.

Peptide data

The peptide data set contains mapped peptide fragments from mass spectrometry (MS) carried out on protein samples from A431 cells. These data were measured by a group at SciLifeLab Stockholm in a ‘proteogenomics’ study where the aim was to discover new genes or gene variants by deep proteomic profiling using an MS method, and mapping the obtained peptides back to the genome. How it was possible to map MS data onto the human genome is explained here.