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Equipment

Illumina NextSeq 550

The NextSeq 550 enables sequencing runs with a capacity of up to 400 million single read or paired-end read sequences. The reading range is either 75 or 150 nucleotides.

With the device, many NGS standard applications can be implemented with small to medium project size. More information about the device specifications can be found in the Illumina data sheet.

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 partition numbers with a massively diverse barcode library to generate >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 in the Technology Brochure of 10x Genomics.

Decentralized sequencer

For NGS projects that are more adaptable to "smaller" devices, such as Amplicon sequencing, targeted resequencing, sequencing of small genomes/transcriptomes (e.g., bacteria, viruses), projects may be realized via so-called "decentralized sequencers". These are devices that are operated by workgroups or institutes at the MHH and to a certain extent have free capacities and can thus be conveyed by the RCUG.

It has been agreed with the responsible device operators that the sharing of their equipment should be requested via the RCUG. For this, please send us a project request.

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Nanodrop ND-1000 spectral photometer

With the Nanodrop nucleic acids can be quantified undiluted 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, the incorporation efficiency of the fluorescent dyes used (Cy3 and Cy5) in the amplified cRNA can also 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

In the hybridization oven, the cRNA populations to be analyzed are hybridized overnight on the microarrays used. 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 for 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 microarray data collected, 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

In the Covaris 220, nucleic acids are sheared by ultrasound into fragments of defined length (150bp - 1000 bp). This is sequence-independent and is a prerequisite for uniform coverage of target sequences in NGS projects (e.g., whole genome, exome, amplicon, metagenome, ChIP-seq). Also, 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 fluoresces (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 worked up.

Software

Our commercial software currently includes:

 

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