Project description

Comparison of total and cytoplasmic RNA expression in three human cell lines

Students: Matilda Berkell, Sauvagya Manna, Matthew The

BACKGROUND:

When RNA is transcribed from DNA in the cell nucleus it goes through some processing before being secreted from the nucleus to the cytoplasm. In the cytoplasm the RNA, often after additional processing, is translated into proteins. Which RNA is secreted out of the nucleus for translation and which are retained is not well understood.

AIM:

To find out if and how RNA expression in the cell nucleus differs from the RNA expression in the cytoplasm. By comparing the RNA expression in the cytoplasm to the total RNA expression the aim is to try and classify the difference in the expression between the cytoplasm and the nucleus. Furthermore the aim is to highlight characteristics of the RNA featured in each compartment.

DATA:

The data consists of Illumina HiSeq2000 single end sequence reads of length 100 bases. In total there are 24 samples from 3 human cell lines (U2OS, A431, U251); 12 samples from the cytoplasm (4 from each cell line) and 12 samples from total RNA (4 from each cell line). Data are available here: /proj/g2015009/cytoplasm/

BRIEF PROJECT OUTLINE:

1. Quality trimming and sequence quality check (deadline 27 Feb)
2. Map trimmed data to reference genome (deadline 27 Feb)
3. Postmap filtering and quality metrics (deadline 4 Mar)
4. Expression quantification (deadline 4 Mar)
5. Differential expression analysis (deadline 9 Mar)
6. Visualization and interpretation of results (deadline 13 Mar)

REFERENCES:

Werne Solnestam, B. et al. Comparison of total and cytoplasmic mRNA reveals global regulation by nuclear retention and miRNAs (2012) 13:574 http://www.biomedcentral.com/1471-2164/13/574

Akan, P. et al. Comprehensive analysis of the genome transcriptome and proteome landscapes of three tumor cell lines. Genome Medicine (2012) 4:86 http://genomemedicine.com/content/4/11/86