Molecular Biology Unit at Core Facility

You can find instruments for molecular biology at Cellkärnan, level 09, at the Cellbiology building. 

Staff are in available to help, see "Contact" below. Tuition fee for external users is 600 SEK.

Cellkärnan user group: Peter Söderkvist (chairman), Henrik Green, Mats Södersröm, Jon Jonasson, Susana Cristobal.


3500 Genetic Analyzer


  • Sequencing
  • Microsatellites
  • LOH
  • SNP

Additional information at


Transgenomic WAVE Nucleic Acid Fragment Analysis System is a fully automatic HPLC-system, designed for applications such as:

  • SNP (Single Nucleotide Polymorphism)
  • Identifying mutations
  • Purification of primers and probes
  • DNA purification

There are two types of columns: DNASepColumn and DNASepHTColumn (High throughput), analysis times are 10 min. and 4 min. respectively.

HPLC columns are sensitive to detergents and other reagents which may be present in PCR reactions. It is therefore very important to follow these instructions. 

PCR reagents compatible with the WAVE system:
AmpliTaq (PE), Taq Gold (PE), Pwo DNA Polymerase (BM), Hot Start Taq (Qiagen), Qiagen Taq DNA Kit, Qiagen Taq PCR Core Kit, Taq Gold (9x), Pfu (1x) (Taq Gold Buffer), Taq DNA Polymerase (Invitrogen, #18038-034), Transgenomic Optimase Polymerase (#703045).
We use 0.2 ml Thermo-Strip (Kebo, #AB-0266).

Do not use these enzymes/kits:
Pure Taq "Ready-To-Go" PCR beads (Amersham)

Additional info

7500 Fast Real-Time PCR system

Applications: Absolut quantification, relative quantification, allele discrimination +/- detection.

Capacity: 96-well fast PCR plates.

Fast PCR reaction can be run in 30-40 min with appropriate mastermix, or in standard mode in 2h with standard mastermix.

Equipped with 5 emission filters for: SYBR® Green I, FAM™, VIC™, JOE™, NED™, TAMRA™, ROX™, Texas Red®, Cy3™, Cy5™.

Further Information at

7900HT Fast Real-Time PCR System

96 fast- or 384-well plate compatibility (the TaqMan® Low Density Array).

Fast PCR option reduces run time to about 35 minutes in a standard 96-well format.

A laser scans and excites the fluorescent dyes in each of the wells.
Continuous wavelength detection from 500-660 nm allows the use of multiple fluorophores in a single reaction.

GS Junior System - 454 Sequencing

System Workflow
One Fragment = One Bead = One Read
The complete sequencing workflow of the GS FLX and GS Junior System comprise of four main steps, leading from purified DNA to analyzed results. The basiic steps include:

  • Generation of a single-stranded template DNA library
  • Emulsion-based clonal amplification of the library
  • Data generation via sequencing-by-synthesis
  • Data analysis using different bioinformatics tools

Sequencing applications

  • Aplicon Sequencing: Targeting sequencing of 10¿s - 100¿s of samples and loci
  • Sequence Capture: Targeted sequencing of custom array regions
  • Whole Genome Sequencning: De novo sequencing and resequencing og microbial organisms (bacteria, fungi, viruses)
  • Metagenomics: Characterization of complex environmental samples; pathogen discovery
  • Transcriptome Sequencing: Full-length sequencing and de novo assembly of transcripts

MiSeq Benchtop Sequencer from Illumina (NGS)

With MiSeq, you can:

  • Multiplex up to 96 samples per run for greater efficiency.
  • Get accurate bi-directional amplicon sequencing.
  • Generate complete de novo assemblies.
  • Produce 2 x 300 paired-end reads and up to 15 Gb of data in a single run.

Agilent Bioanalyzer 2100

Users buy their own kits.

Affymetrix Microarray

Additional Information at

FUJIFILM imager FLA-5000

Instrument for scanning gels, i.e. 2D electrophoresis gels. Scanning surface is 40 x 46 cm with a resolution of 25 µm per pixel.

Detection methods:

  • Fluoroscence
  • Chemiluminescence
  • Isotopes

QIAGEN Tissue Lyser

For high-throughput disruption of a wide range of biological samples

  • Fast - disruption of up to 48 samples in as little as 2-4 minutes
  • Disruption is achieved through the beating and grinding effect of beads
  • Cross-contamination-free – closed system prevents tube-to-tube carryover
  • Reproducible – highly standardized disruption methods
  • Flexible – compatible with different sample types and disruption buffers
  • Integrated – part of QIAGEN’s tissue-management system from collection/stabilization to purification

You have to buy your own QIAGEN kits and Beads, suitable for use with the TissueLyser system.

Additional information at

epMotion 5070

epMotion 5070 is a pipetting robot that allows users to write their own programs for preparing 96-well plates for PCR. Two pipettes are available, 1-50ul and 40-1000ul. Tips are purchased by individual users separately.

Biomek 2000

Pipetting robot.

Quantus Fluorometerquantus

A sensitive single tube fluorometer for fluorescence based quantitation of DNA and RNA. Fluorescence-based nucleic acid quantification methods are more sensitive than absorbance-based methods, allowing you to quantitate low-level DNA samples accurately.

PyroMark (Klinisk farmakologi, building 420)

To operate the instrument, you must undergo training to get a operator license. A list of persons entitled to complete the education is at the instrument.  Please contact: Malin Lindqvist Appell, tel 013-286880,

PyroMark Q96 MD

PyroMark is a real-time sequencing equipment based on pyrosequencing where 96 samples are sequenced in parallel. Reading lengths around 30-50 bases from the first base after sequencing primer. One clear advantage is that you get a pyramid as quality control.

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