Equipment

Illumina NextSeq 550
10x Genomics Chromium Single Cell Controller
Decentralized sequencers
Nanodrop ND-1000 spectral photometer
Agilent 2100 Bioanalyzer
Agilent hybridization oven
Agilent Microarray Scanner G2565CA
ABI 7500 FAST Real-Time PCR
Covaris 220
Qubit 2.0
SpeedVac
Software

Illumina NextSeq 550

The NextSeq 550 enables sequencing runs with a capacity of up to 400 million single or paired-end reads. The possible reading range covers a maximum of 75 or 150 nucleotides from only one end or both ends of the unknown insert.
This sequencer enables the implementation of many NGS standard applications for small to medium project sizes. More information about the device specifications can be found in the Illumina data sheet.

For sequencing projects that can be better implemented on sequencers other than our NextSeq550, these projects can be implemented using so-called "decentralized sequencers". These are devices that are operated by various working groups or institutes of the MHH and have a certain amount of free capacity and can therefore be arranged for shared use.

10x Genomics Chromium Single Cell Controller

The Chromium Single Cell Gene Expression Solution provides a comprehensive, scalable solution for cell characterization and gene expression profiling of hundreds to tens of thousands of cells.

The compact, sleek Chromium Controller rapidly and efficiently combines large numbers  of partitions with a massively diverse barcode library and generates >100,000 barcode-containing partitions in a matter of minutes. The Chromium Controller allows the application of any Chromium Solution, from genome to single cell analysis. More information about the technology can be found at 10x Genomics.

Decentralized sequencers

For sequencing projects that can be better implemented on sequencers other than our NextSeq550, these projects can be implemented using so-called "decentralized sequencers". These are devices that are operated by various working groups or institutes of the MHH and have a certain amount of free capacity and can therefore be arranged for shared use.
It has been agreed with the responsible device operators that the joint use of their devices should be requested via the RCUG. For this, please send us a project request.

Nanodrop ND-1000 spectral photometer

Nanodrop spectral photometer allows quantification of undiluted nucleic acids within a concentration range of ~ 10-3000 ng/μl in a volume of 1-2 μl. By absorption measurements at 550 nm and 650 nm, also the incorporation efficiency of the fluorescent dyes (Cy3 and Cy5) in the amplified cRNA can be determined.

Agilent 2100 Bioanalyzer

The bioanalyzer determines the quality / integrity of the total RNA. In addition, the fragment length profile of amplified cRNA or cDNA samples can be analyzed. Another important area of application is the quality control of various libraries (fragment length profile) for NGS-based applications. The RCU Genomics operates 2 bioanalyzers, one in the Transcriptomics and one in the Genomics subunit.

Agilent hybridization oven

The hybridization oven is used to hybridize cRNA populations onto microarrays overnight. A maximum of 48 slides can be hybridized in parallel.

Agilent Microarray Scanner G2565CA

The microarray laboratory is equipped with a G2565CA scanner with a maximum resolution of 2 μm. This scanner allows automated high-throughput processing of up to 48 glass slide-based microarray slides each containing up to 1 million probes.

ABI 7500 FAST Real-Time PCR

The Real-Time PCR cycler enables us to verify certain aspects of collected microarray data, or to contribute to a selective deepening of the information content. We routinely use TaqMan-based assays from Applied Biosystems to quantify individual transcripts or specific splice variants.

Covaris 220

The Covaris 220 shears nucleic acids by ultrasound into fragments of defined length (150bp - 1000 bp). This process is sequence-independent and is a prerequisite for uniform coverage of target sequences for NGS projects (e.g., whole genome, exome, amplicon, metagenome, ChIP-seq). Moreover, the device may be used for the quantitative digestion  of sample material (e.g., for metagenomics).

Qubit 2.0

The qubit fluorimeter enables the selective, quantitative determination of single nucleic acid species (dsDNA, ssDNA, RNA). In contrast to the nanodrop which measures the total amount of nucleic acids in a sample, specific, intercalating dyes ensure that only the nucleic acid species under investigation fluoresce (signal strengths of other species are up to 1000x lower). The ratio of the measured concentrations of qubit and nanodrop is a measure of the purity and integrity of the nucleic acids in a sample.

SpeedVac

Often, the sample material is present after purification in very low concentrations (e.g., after ChIP enrichments, small RNA). In a vacuum concentrator volumes can be gently reduced in a short time without strong heating, so that this material can be processed further.

Software

Our commercial software currently includes:

  • Feature Extraction (Agilent Technologies)
  • ImaGene (BioDiscovery Inc.)
  • GeneSpring (Agilent Technologies)
  • Omics Explorer (Qlucore)
  • StrandNGS (Avadis)
  • IPA (Qiagen)
  • SigmaPlot (Systat Software, Inc.)

 

To optimize our analysis capabilities, we also develop custom tools using:

  • Microsoft Excel (Visual Basic)
  • R and Bioconductor
  • Eclipse (Java)