Omics platforms - Transcriptomics

Short description:

The Omics platform Transcriptomics mainly aims at the identification, quantification and characterization of long and short non-coding RNAs from a range of samples like human or animal body fluids, tissues, or cells, environmental or microbial samples. Additionally, the platform is frequently used for de-novo genome sequencing and characterization of nucleic-acid protein interactions, e.g. using ChIPseq. The platform comprises equipment for ultra-high-throughput sequencing, library preparation for transcriptomics, genome resequencing, genome de-novo sequencing and ChIPseq. High-throughput sequencing generates large datasets and demands computationally intensive data analyses. The Transcriptomics platform therefore provides several software pipelines that enable efficient and standardized data processing using the UFZ high performance computing infrastructure.

Major research issues/sites:

The Helmholtz-University Young Investigators Group “Bioinformatics and Transcriptomics” studies disease relevant differentiation processes of immune cells. The group aims at elucidating the link between non-protein coding RNAs and epigenetic modifications in response to Th cell differentiation. It strives to gain a systems biology perspective of this differentiation process. The group investigates how environmental toxicants affect the epigenome of immune cells and whether long non-coding RNAs are involved in this process. It combines bioinformatic and experimental competencies, relying mainly on transcriptomic, epi- and genomic high-throughput methods and on bioinformatic approaches to analyze and integrate these data.

Selected publications:

Rivarola-Duarte L, Otto C, Jühling F, Schreiber S, Bedulina D, Jakob L, Gurkov A, Axenov-Gribanov D, Sahyoun AH, Lucassen M, Hackermüller J, Hoffmann S, Sartoris F, Pörtner HO, Timofeyev M, Luckenbach T, Stadler PF. A first Glimpse at the genome of the Baikalian amphipod Eulimnogammarus verrucosus. J. Exp. Zool. B. 322(3):177-89. 2014. | DOI: 10.1002/jez.b.22560

Hoffmann S, Otto C, Doose G, Tanzer A, Langenberger D, Christ S, Kunz M, Holdt L, Teupser D, Hackermüller J, Stadler PF. A multi-split mapping algorithm for circular RNA, splicing, trans-splicing, and fusion detection. Genome Biology 15:R34. 2014.

Hoffmann S,  Otto C,  Kurtz S,  Sharma CM,  Khaitovich P, Vogel J, Stadler PF, Hackermüller J. Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures. PLoS Comput Biol 5: e1000502. 2009.

Short technical description:

The platform comprises

  • Illumina Hiseq 2000 ultra-highthroughput sequencer
  • Instrumentation for library preparation for short and long RNAseq, genome sequencing, targeted re-sequencing, ChIPseq and Clipseq
  • UFZ high performance computing cluster eve with currently more than 2400 cores and greater 400 terabytes of storage
  • Software pipelines for the efficient processing of data e.g. for
    • De novo transcript assembly
    • Differential expression of transcripts
    • Identification of alternative transcript structures
    • Genome assembly

Options and conditions for visiting scientists:

Available for joint projects if (co)-funding for consumables is available.

Unit Cost of use and principles of costing:

Costs apply for library preparation and sequencing consumables and need to be estimated for specific projects.

centre running the infrastructure:

UFZ - Helmholtz Centre for Environmental Research

type of facility:

Laboratory / high-end instrument


  • UFZ - Helmholtz Centre for Environmental Research
  • Phone: +49 341 235-0