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Analysis of:

  • Transcriptome analysis by RNA-seq (mRNA, lncRNA, medium-sized RNA, smallRNA)
  • Translation control by Ribo-seq 
  • Binding/occupancy analysis by ChIP- or CLIP-seq
  • Genome analysis using Whole Genome-seq or Exom-seq 
  • Oxford Nanopore DNA-/RNA-Seq data

Primary analyses

  • Quality control of raw data
  • Removal of adapter sequences and quality trimming
  • Mapping (assignment of reads to known reference genomes)
  • Annotation (assignment of mapped reads to known genes)
  • Determination of read coverage
  • Normalization (regarding RNA composition, transcript length, differential expression, etc.)

Secondary analyses

  • Determination of differential gene expression
  • Correlation of mRNA and miRNA expression (including target analyses)
  • Determination of alternative isoforms (due to , e.g., alternative splicing)
  • Quantification of translation efficiency (Ribo-seq)
  • Evaluation of binding profiles (ChIP- or CLIP-Seq)
  • Determination of effector pathways using gene annotation enrichment analysis (GAEA) and gene set enrichment analysis (GSEA)
  • Meta gene analyses, inclusion of "public data" (eg TCGA) and further analyses on request 

Nanopore Sequencing

  • Support for Oxford Nanopore Sequencing
  • Optional library preparation (barcoded)
  • Data analysis

Prices

Prices for evaluation and further analysis of NGS data on knwon genomes.

 

ServiceMed. Fak.

MLU (no member of Med. Fak)

Billing Unit

30€50€per conversation
Quality control of small RNA (RIN)55€70€

per chip (max. 11 samples/chip)

Quality control of RNA (RIN)40€50€per chip (11-12 samples/chip)
Data download5€5€per 10 GB of data¹
Primary analysis10€20€per 20 Mio. reads¹
Secondary analysis25€30€per analysis

  ¹ Per started billing unit.

Storage of data for 3 months.

 

ContactDanny MisiakMarkus Glaß

 

Publications

Müller S, Glaß M, Singh AK, Haase J, Bley N, Fuchs T, Lederer M, Dahl A, Huang H, Chen J, Posern G, Hüttelmaier S. IGF2BP1 promotes SRF-dependent transcription in cancer in a m6A- and miRNA-dependent manner. Nucleic Acids Res. 2018 Oct 29. doi: 10.1093/nar/gky1012. [Epub ahead of print] PubMed PMID: 30371874.

Minocha R, Popova V, Kopytova D, Misiak D, Hüttelmaier S, Georgieva S, Sträßer K. Mud2 functions in transcription by recruiting the Prp19 and TREX complexes to transcribed genes. Nucleic Acids Research, gky640, https://doi.org/10.1093/nar/gky640.

Müller S, Bley N, Glaß M, Busch B, Rousseau V, Misiak D, Fuchs T, Lederer M, Hüttelmaier S. IGF2BP1 enhances an aggressive tumor cell phenotype by impairing miRNA-directed downregulation of oncogenic factors. Nucleic Acids Res. 2018 Jul 6;46(12):6285-6303. doi: 10.1093/nar/gky229. PubMed PMID: 29660014.

Zhou F, Liu Y, Rohde C, Pauli C, Gerloff D, Köhn M, Misiak D, Bäumer N, Cui C, Göllner S, Oellerich T, Serve H, Garcia-Cuellar MP, Slany R, Maciejewski JP, Przychodzen B, Seliger B, Klein HU, Bartenhagen C, Berdel WE, Dugas M, Taketo MM, Farouq D, Schwartz S, Regev A, Hébert J, Sauvageau G, Pabst C, Hüttelmaier S, Müller-Tidow C. AML1-ETO requires enhanced C/D box snoRNA/RNP formation to induce self-renewal and leukaemia. Nat Cell Biol. 2017 Jul;19(7):844-855. doi: 10.1038/ncb3563. Epub 2017 Jun 26. PubMed PMID: 28650479.

Busch B, Bley N, Müller S, Glaß M, Misiak D, Lederer M, Vetter M, Strauß HG, Thomssen C, Hüttelmaier S. The oncogenic triangle of HMGA2, LIN28B and IGF2BP1 antagonizes tumor-suppressive actions of the let-7 family. Nucleic Acids Res. 2016 Feb 24. pii: gkw099. [Epub ahead of print] PubMed PMID: 26917013.

Köhn M, Ihling C, Sinz A, Krohn K, Hüttelmaier S. The Y3** ncRNA promotes the 3' end processing of histone mRNAs. Genes Dev. 2015 Oct 1;29(19):1998-2003. doi: 10.1101/gad.266486.115. PubMed PMID: 26443846; PubMed Central PMCID: PMC4604341.

Braun J, Misiak D, Busch B, Krohn K, Hüttelmaier S. Rapid identification of regulatory microRNAs by miTRAP (miRNA trapping by RNA in vitro affinity purification). Nucleic Acids Res. 2014 Apr 1;42(8):e66. doi: 10.1093/nar/gku127. Epub 2014 Feb 7. PubMed PMID: 24510096; PubMed Central PMCID: PMC4005655.

 

 

Charles-Tanford Proteinzentrum
Kurt-Mothes-Str. 3A
06120 Halle

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Contact:
Dr. Markus Glaß
Dipl.-Bioinf Danny Misiak

office: 1.13.0
mail: cfi(at)medizin.uni-halle.de 
phone.: +49-345-557 3962

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