Project Design

An important step to successful gene expression analysis is the proper design of a detailed project plan. Thus, as an initial step, we evaluate the experimental question together with our users. Thereby we aim to optimize the experimental setup to obtain high quality material and statistical relevance. The following questions must be answered :

  • What is the experimental question?
  • How is this experimental question best translated into a statistically relevant and cost effective setup?
  • Which samples should be used and how many of them are necessary to  obtain a robust result?
  • How are these samples collected?
  • Which RNA isolation technique is optimal?
  • How is RNA integrity achieved?
  • Which platform/technique should be applied?

* Protocols, material and equipment, as well as practical training, is  provided by the facility.

MICROARRAYS

  • AGILENT MICROARRAY PLATFORM : Cy5 labeled RNA/DNA target molecules are extremely sensitive to oxidation. Therefore we process all microarrays in an ozone free environment (hybridization, washing and scanning). This protects the dye from oxidation thus yielding reliable results. Cy3 and Cy5 intensities are detected by simultaneous two-color scanning using an Agilent DNA microarray scanner at 2-5 micron resolution.

  • AFFYMETRIX MICROARRAY PLATFORM : The GeneChip® Scanner 3000 7G is a product extension of the GeneChip® Scanner 3000 series that allows nextgeneration higher density arrays, enabling new applications for genotyping with up to 500,000 SNPs, tiling arrays for transcription, and all-exon arrays for wholegenome analysis. The fluidic operations performed on the Affymetrix GeneChip® cartridges are crucial to the delivery of high-quality results. The Fluidics Station 450 from Affymetrix incorporates new features and important design improvements to  enhance the operation and performance of the GeneChip system.

Microarray- Applications include:

  • Genome Expression Analysis on 3' arrays
  • Exon 1.0 ST arrays /Gene 1.0 ST arrays
  • miRNA arrays
  • Genotyping and comparative genomic hybridization
  • (SNP) arrays
  • DNA Methylation arrays
  • Chromatin ImmunoPrecipitation arrays (ChIP-on-chip)

Project Inquiry
The platform and array design to be used vary according to the biological question. For your specific microarray project, please contact us for detailed information concerning price, starting material, protocols available and microarray data analysis by sending us an e-mail to talatgwdgdotde or contact us directly : Tel : 0049-551-3922316

Sample Shipment

Developmental Biochemistry
Microarray and Deep-Sequencing Core Facility (UMG)
Justus-von-Liebig-Weg 11
37077 Göttingen, Germany

RNA/DNA QUALITY CONTROL

  • FRAGMENT ANALYZER: is used and recommended as an automated capillary electrophoresis system for the quantification and qualification of NGS libraries, gDNA and RNA giving the power to optimize runs for speed or resolution. Capillaries are auto-flushed between runs to eliminate cross contamination and further underline data integrity. The instrument resolves fragments from 10 bp to 40,000 bp, get resolution down to 2 bp for fragments and allow detection starts at 5 pg/μL.
  • AGILENT BIOANALYZER 2100 : A microfluidics-based platform for sizing, quantification and quality control of DNA and RNA. For RNA, the Bioanalyzer software produces a RIN (RNA Integrity Number) that allows a comparison of sample quality.

  • PIPPIN PREP : is a system that separates DNA using agarose gel electrophoresis, and then electroelutes DNA fractions according user-input fragment size ranges. This virtually eliminates the labor required for manual prep gels, and provides a higher quality sample for NGS.

  • BIORUPTOR NGS : is a tool for NGS library preparation. This cutting-edge sonication device is dedicated exclusively to fast DNA shearing and provides you suitable DNA for unbiased library preparation prior to next generation sequencing.

NEXT GENERATION SEQUENCING (NGS)

    • HiSEQ 4000 : the HiSeq 4000 is based on innovative patterned flow cell technology, which offers an exceptional level of throughput for diverse sequencing applications.

      Patterned flow cells contain billions of nanowell substrates at fixed locations across both surfaces of the flow cell. The structured organization provides even spacing of sequencing clusters to deliver significant increases in sequencing reads and total output of the system. Offering ultra-high throughput, the HiSeq 4000 generates >400 Gb per day and up to 1.5 Tb per run (3,5 days). This power allows sequencing of more samples at greater depth, generating richer, more meaningful data in less time

    • MISEQ SYSTEM : a fully integrated personal sequencer, delivering a streamlined solution that takes you from rapid sample prep through automated data analysis and storage in the BaseSpace cloud. This system performs both single and paired-end runs with read lengths of up to 2 x 300 base pairs (7.5-8.5 Gb) per run. This platform also leverages a new proprietary protocol for efficient and cost-effective targeting of 10-100 amplicons.

    NGS- Applications include:

    • Whole Genome Sequencing
    • De Novo Sequencing, Resequencing
    • Chromatin IP analysis (ChIP-Seq)
    • Transcriptome Analysis (RNA-Seq)
    • Small RNA Identification and Quantitation
    • DNA Methylation analysis
    • Metagenomics


    Project Inquiry
    A number of parameters vary according to the type of application on the HiSeq 2000 or the MiSeq system. For your specific sequencing project, please contact us for detailed information concerning price, starting material, targeted number of reads and sequence data analysis by sending us an e-mail to talatgwdgdotde or contact us directly : Tel : 0049-551-3922316

    Sample Shipment

    Developmental Biochemistry
    Microarray and Deep-Sequencing Core Facility (UMG)
    Justus-von-Liebig-Weg 11
    37077 Göttingen, Germany

    NANOSTRING

    The nCounter® Analysis System is ideally suited to study defined gene sets in a large sample set, e.g. validation of microarray experiments or specific expression signatures. The technology is based on direct, multiplexed measurement of gene expression without amplification, utilizing molecular barcodes and single molecule imaging to identify and count hundreds of transcripts in a single reaction.


    Technology

    • Nanostring nCounter Gene Expression Analysis System nCounter Prep Station is the automated fluidic handling component of the nCounter Analysis System. It processes samples post-hybridization to prepare them for data collection on the nCounter Digital Analyzer. Prior to placing samples on the Prep Station, samples need to be hybridized according to the nCounter protocol. On the deck of the Prep Station, hybridized samples are purified and subsequently immobilized in the sample cartridge for data collection.


    Our portfolio of application-specific solutions currently includes kits for gene expression, copy number variation and miRNA analysis. To select a specific application click here (http://www.nanostring.com)

    Sample Shipment

    Microarray and Deep-Sequencing Core Facility
    University Medical Center Göttingen (UMG)
    Justus-von-Liebig-Weg 11
    37077 Göttingen, Germany

    BIOINFORMATICS SERVICES

    Standard Bioinformatics
    For experienced users we offer direct access to fastq files of demultiplexed samples providing data at a very basal level. Data processing of fastq files will need expertise for quality assessment, read mapping, counting and further analysis.

    Advanced Bioinformatics
    For the majority of users we provide a primary data analysis typically inferring a list of differentially expressed genes between different experimental sets. In a first step, sequence reads will be demultiplexed, i.e. bar codes resolved for each sample, and reads are recorded along with quality phred scores as fastq files. Subsequently, the d to the transcriptome of the appropriate reference organism(s) by time-efficient mapping tools. Hereby, the amount of  mapped/unmapped reads as well as the coverage of known genes are captured. Finally, read counts per gene are summarised and normalisation factors are calculated correcting for total library size. Single gene expression are tested for statistical significance which comprises the estimation of data dispersion and negative binomial testing. For more complex experimental designs generalised linear models are applied for attributing multivariate analysis.

    In case of leaving standard procedures either for laboratory protocols or statistical analysis and visualisation, we would operate on cooperation basis.