Core Facilities

heinz-himmelbauer
Genomics Unit

Unit Structure

HEAD OF THE UNIT:
Heinz Himmelbauer
LABORATORY MANAGER:
Anna Ferrer
LABORATORY TECHNICIANS:
Anna Menoyo (maternity leave from June 2013), Maik Zehnsdorf, Núria Andreu, Irene González, Maria Aguilar, Magda Montfort
BIOINFORMATICIANS:
Debayan Datta, Manuela Hummel (until September 2013), Sarah Bonnin (on sabbatical until July 2013), Juliane Dohm (MPI Berlin), André Minoche (MPI Berlin), Sarah Jäger (MPI Berlin, until July 2013), André Gohr (MPI Berlin, from December 2013)

Summary

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 (one newly installed in 2013) and one Roche/FLX sequencer. In 2013, the Unit performed 85 runs on Illumina HiSeq sequencing instruments (+33%). 32 sequencing runs were performed on the Roche/FLX sequencer (+52%). The Unit also 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.
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Research Projects

  • Implementation of improved sequencing library preparation methodologies for application such as pooled ChIP-Seq library sequencing, mate-pair sequencing, and directional transcript sequencing.
  • Implementation of automation for the preparation of sequencing libraries on a Tecan robotic platform
  • Implementation of transcriptome sequencing from pools of few cells and from single cells
  • Development of a robust framework for genome sequencing and genome assembly.

Selected Publications

  1. Dohm JC, Minoche AE, Holtgräwe D, Capella Gutiérrez S, Zakrzewski F, Tafer H, Rupp O, Rosleff Sörensen T, 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, doi: 10.1038/nature12817. Epub 2013 Dec 18.
  2. Ibarra-Laclette E, Lyons E, Hernández-Guzmán G., Pérez-Torres CA, Carretero-Paulet L, Chang TH, Lan T, Welch AJ, Abraham Juárez MJ, Simpson J, Fernández-Cortés A, Arteaga-Vázquez M, Góngora-Castillo E, Acevedo-Hernández G, Schuster SC, Himmelbauer H, Minoche AE, Xu S, Lynch M, Oropeza-Aburto ., Cervantes-Pérez SA, de Jesús Ortega-Estrada M, Cervantes-Luevano JI, Michael TP, Mockler T, Bryant D, Herrera-Estrella A, Albert VA, Herrera-Estrella L.
    “Architecture and evolution of a minute plant genome.”
    Nature, 498(7452):94-8 (2013).
  3. Weber B, Heitkam T, Holtgräwe D, Weisshaar B, Minoche AE, Dohm J, Himmelbauer H, Schmidt T.
    “Highly diverse chromoviruses of Beta vulgaris are classified by chromodomains and chromosomal integration.”
    Mobile DNA, 4(1):8 (2013).
  4. Llorens F, Hummel M, Pantano L, Pastor X, Vivancos A, Castillo E, Mattlin H, Ferrer A, Ingham M, Noguera M, Kofler R, Dohm JC, Pluvinet R, Bayes M, Himmelbauer H, del Rio JA, Martí E, Sumoy L.
    “Microarray and deep sequencing cross-platform analysis of the mirRNome and isomiR variation in response to epidermal growth factor.”
    BMC Genomics, 14(1):371-371 (2013).
  5. Jiménez-Guri E, Huerta-Cepas J, Cozzuto L, Wotton KR, Kang H, Himmelbauer H, Roma G, Gabaldón T, Jaeger J.
    “Comparative transcriptomics of early dipteran development.”
    BMC Genomics, 14(1):123-123 (2013).