Deep Seq: Next Generation Sequencing Facility
  

Projects

Publications:

1. Brown WR, Thomas G, Lee NC, Blythe M, Liti G, Warringer J, Loose MW. (2014) Kinetochore assembly and heterochromatin formation occur autonomously in Schizosaccharomyces pombe. Proc Natl Acad Sci U S A. 2014  4;111(5):1903-8.

2. Moreton J, Malla S, Aboobaker AA, Tarlinton RE, Emes RD (2014) Characterisation of the horse transcriptome from immunologically active tissues. PeerJ. Accepted for publication.

3. Amer AHA, Wall RJ, Malla S, Sang F, Aboobaker A, Avery SV, Mellor IR, Rose M, Rowlands CJ, Grant TW, Bell DR (2014) Genes involved in the induction of liver growth by peroxisome proliferators. Toxicology research. Accepted for publication. 

4. Hawkins, M., Malla, S., Blythe, M.J., Nieduszynski, C. A., Allers, T. (2013) Accelerated growth in the absence of DNA replication origins. Nature. Nov 28; 503 (7477): 544-7

5. Hamilton, H.M., Wilson, R., Blythe, M., Nehring, R.B., N.C., Fonville, Louis, E.J., Rosenberg, S. M. (2013) Thymineless death is inhibited by CsrA in Escherichia coli lacking the SOS response. DNA Repair 12: 993–999.

6. Mahdavi J, Royer PJ, Sjölinder HS, Azimi S, Self T, Stoof J, Wheldon LM, Brännström K, Wilson R, Moreton J, Moir JW, Sihlbom C, Borén T, Jonsson AB, Soultanas P, Ala'aldeen DA. (2013) Pro-inflammatory cytokines can act as intracellular modulators of commensal bacterial virulence. Open Biol. Oct 9; 3(10): 130048.

7. Müller CA, Hawkins M, Retkute R, Malla S, Wilson R, Blythe MJ, Nakato R, Komata M, Shirahige K, de Moura AP, Nieduszynski CA. (2013)  The dynamics of genome replication using deep sequencing.  Nucleic Acids Res. Jan; 42(1): e3

8. Jaber-Hijazi F, Lo PJ, Mihaylova Y, Foster JM, Benner JS, Tejada-Romero B, Chen C, Malla S, Solana J, Ruzov A, Aboobaker AA (2013) Planarian MBD2/3 is required for adult stem cell pluripotency independently of DNA methylation. Dev Biol. Dec 1; 384(1): 141-53

9. Ries L, Pullan ST, Delmas S, Malla S, Blythe MJ, Archer DB (2013) Genome-wide transcriptional response of Trichoderma reesei to lignocellulose using RNA sequencing and comparison with Aspergillus niger. BMC Genomics. Aug 9; 14: 541

10. Kamila D, Blythe MJ, Malla S, Diane GP, Alessandro G, Pavan P, Moles A, Snart C, Ryder T,  Ortori CA, Barrett DA, Schuster E, Stöger R (2013) Transient exposure to low levels of insecticide affects metabolic networks of honeybee larvae. Plos One.  Jul 2; 8(7): e68191

11. Novodvorska M,  Hayer K,  Pullan ST, Wilson R, Blythe MJ, Hein S, Stratford M, Archer DB (2013) Trancriptional landscape of Aspergillus niger at breaking of conidial dormancy revealed by RNA-sequencing.  BMC Genomics. 14:246.

12. Liti G, Nguyen AN, Blythe M, Müller CA, Bergström A, Cubillos FA, Calas FD, Khoshraftar S, Malla S, Mehta N, Siow CC, Warringer J, Moses AM, Louis EJ, and Nieduszynski CA (2013) High Quality de novo Sequencing and Assembly of the Saccharomyces arboricolus genome.  BMC Genomics. Jan 31; 14: 69.

13. Brown K, Moreton J, Malla S, Aboobaker AA, Emes RD, Tarlinton RE (2012) Characterisation of retroviruses in the horse genome and their transcriptional activity via transcriptome sequencing. Virology. 433(1): 55-63.

14. Delmas S, Pullan ST, Gaddipati S, Kokolski M, Malla S, Blythe MJ, Ibbett R, Campbell M, Liddell S, Aboobaker A, Tucker GA and Archer DB (2012) Uncovering the genome-wide transcriptional responses of the filamentous fungus Aspergillus niger to lignocellulose using RNA sequencing. PLoS Genetics 8(8): e1002875.

15. Blythe M, Malla S, Everall R, Shih Y-h, Lemay V, Moreton J, Wilson R and Aboobaker AA (2012) High Through-Put Sequencing of the Parhyale hawaiensis mRNAs and microRNAs to Aid Comparative Developmental Studies. PLoS ONE 7(3): e33784. 

16. Solana J, Kao D, Mihaylova Y, Malla S, Wilson R, Aboobaker AA, (2011) Defining the molecular profile of planarian pluropotent stem cells using a combinatorial RNA-seq, RNAi and irradiation approach. Genome Biology, 22; 13(3): R19 

17. Hooton SPT, Timms AR, Rowsell J, Wilson R and Connerton IF (2011) Salmonella Typhimurium-specific bacteriophage PhiSH19 and the origins of species specificity in the Vi01-like phage family. Virology Journal 8: 498.

18. Blythe MJ, Kao D, Malla S, Rowsell J, Wilson R, Evans, D, Jowett, J, Hall, A, Lemay, V, Lam, S and Aboobaker AA, (2010) A Dual Platform Approach to Transcript Discovery for the Planarian Schmidtea Mediterranea to Establish RNAseq for Stem Cell and Regeneration Biology. PLoS One 5(12).

Publications with acknowledgement:

1. Evans T, Wade CM, Chapman FA, Johnson AD, Loose M (2014) Acquisition of germ plasm accelerates vertebrate evolution. Science. Apr 11; 344(6180): 200-3.

2. Kao D, Felix D, Aboobaker AA (2013) The planarian regeneration transcriptome reveals a shared but temporally shifted regulatory program between opposing head and tail scenarios. BMC Genomics. Nov 16; 14: 797.

Deep Seq

Centre for Genetics and Genomics
The University of Nottingham
Queen's Medical Centre, Nottingham, NG7 2UH

telephone: +44 (0) 115 823 0363
email: deep.seq@nottingham.ac.uk