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Genomics Unit



HEAD OF THE UNIT:
Heinz Himmelbauer
LABORATORY MANAGER:
Anna Ferrer
LABORATORY TECHNICIANS:
Anna Menoyo, Irene González, Magda Montfort, Maik Zehnsdorf, Maria Aguilar (maternity leave from October 2014), Núria Andreu
BIOINFORMATICIANS:
Sarah Bonnin (until October 2014), Kathrin Meindl (from September 2014), Juliane Dohm (MPI Berlin), André Minoche (MPI Berlin, until September 2014), André Gohr (MPI Berlin, until November 2014)

Summary


Fig. 1 Illumina synthetic long reads (moleculo technology) for the discovery of genome variation.


Fig. 2 Analysis of E. coli Illlumina read data generated from low-amount sequencing libraries.

The scope of the Genomics Unit is to provide excellent, state-of-the-art services in the fields of microarray technology and next-generation sequencing. In addition to providing service, the Unit performs its own research in the genomics field and is dedicated to test, implement, and to develop new protocols (wet lab and bioinformatics) to advance the analysis of genes and genomes. The Unit is equipped with two Illumina HiSeq instruments, and handles requests of CRG scientists for Illumina MiSeq sequencing and for Sanger sequencing. The Unit has set up protocols for genomic sequencing, exome selection, amplicon sequencing, ChIP-Seq, and transcriptome characterization at the level of total RNA, small RNA, or mRNA.


Research Projects

  • Improvement of sequencing library preparation procedures for various applications.
  • Implementation of transcriptome sequencing protocols from single cells.
  • Testing of innovative sequencing concepts and platforms (wet lab and bioinformatics).
  • Genome bioinformatics.

Selected Publications

Holtgräwe D, Sörensen TR, Viehöver P, Schneider J, Schulz B, Borchardt D,
Kraft T, Himmelbauer H, Weisshaar B.
“Reliable in silico identification of sequence polymorphisms and their application for extending the genetic map ofsugar beet (Beta vulgaris).”
PLoS One, 9:e110113. doi:10.1371/journal.pone.0110113 (2014).

Olalde I, Sánchez-Quinto F, Datta D, Marigorta UM, Chiang CW, Rodríguez JA,
Fernández-Callejo M, González I, Montfort M, Matas-Lalueza L, Civit S, Luiselli
D, Charlier P, Pettener D, Ramírez O, Navarro A, Himmelbauer H, Marquès-Bonet T,
Lalueza-Fox C.
“Genomic analysis of the blood attributed to Louis XVI (1754-1793), king of France.”
Sci Rep, 4:4666. doi: 10.1038/srep04666 (2014).

Dohm JC, Minoche AE, Holtgräwe D, Capella-Gutiérrez S, Zakrzewski F, Tafer H,
Rupp O, Sörensen TR, Stracke R, Reinhardt R, Goesmann A, Kraft T, Schulz B,
Stadler PF, Schmidt T, Gabaldón T, Lehrach H, Weisshaar B, Himmelbauer H.
“The genome of the recently domesticated crop plant sugar beet (Beta vulgaris).”
Nature, 505:546-9. doi: 10.1038/nature12817 (2014).

Heitkam T, Holtgräwe D, Dohm JC, Minoche AE, Himmelbauer H, Weisshaar B,
Schmidt T.
“Profiling of extensively diversified plant LINEs reveals distinct plant-specific subclades.”
Plant J, 79:385-97. doi: 10.1111/tpj.12565 (2014).

Zakrzewski F, Schubert V, Viehoever P, Minoche AE, Dohm JC, Himmelbauer H,
Weisshaar B, Schmidt T.
“The CHH motif in sugar beet satellite DNA: a modulator for cytosine methylation.”
Plant J, 78:937-50. doi: 10.1111/tpj.12519 (2014).