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Cellkärnan (Molecular Biology Unit)

 Cellk

Cellkärnan is located on floor 09 in the cell biology building.
Cellkärnan lab tel: 010-1032682
.

Staff

Molecular Biology:

Annette Molbaek, tel: 010-1032663
Åsa Schippert, tel: 010-1032663
Mats Söderström, tel: 010-1033190

Training fee for external users: 600 sek.

Pharmacology (PyroMark)

Henrik Green, tel: 010-1031544
Malin Linqvist-Appell, tel: 010-1031229

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


Molecular Biology Instruments:


3500 Genetic Analyzer

3500 8-Bild1capillary platform:

Applications:
• Sequencing
• Microsatellites
• MLPATM
• LOH
• SNP
Additional information at www.appliedbiosystems.com

 
Fees:
Internal user: Basic Fee: 1-8 samples/run : 15 sek/sample, max. 80 sek. (includes polymer, buffers and plastics). > 8 samples/run : 10 sek/sample (includes polymer, buffers and plastics).
External user: Basic Fee: 30 sek/sample (includes polymer, buffers and plastics).


Sequencing:
• You may elect to purchase reagents and perform everything yourself and only pay the basic fee.
• You may elect to purchase reagents from Cellkärnan but perform the sequencing yourself, 70sek/sample, includes Big Dye Terminator reagent, Exo-SAP-IT, "post reaction clean up" by Cellkärnan staff.
• You may elect to provide template and primer and hire Cellkärnan staff to perform the sequencing for you; 130sek/sample, includes sequencing reactions, Big Dye Terminator reagent, Exo-SAP-IT, "post reaction clean up" by Cellkärnan staff.
• Only "post reaction clean up" by Cellkärnan staff: 10 sek/sample.

Reservation of Instrument


WAVE

Transgenomic WAVE Nucleic Acid Fragment Analysis System is a fully automatic HPLC-system, designed for applications such as:Wave
• 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 www.transgenomic.com

Fees: 
Do it yourself: 300 sek/run + 5 sek/sample (injection)
Analysis assistance: 600 sek/run + 5 sek/sample (injection)
External user: 800 sek/run + 5 sek/sample (injection)
Special analysis like Primer Extension is 10 sek/sample (injection).
If you need to use the HSX-detektorn (incl staining solution) there's an additional fee of 100 sek and 5 sek/sample (injection).

Reservation of Instrument


7500 Fast Real-Time PCR system

 

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

Capacityt: 96-well fast PCR plates.7500

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 www.appliedbiosystems.com

External user: 200 sek/plate.

Reservation of Instrument

7900HT Fast Real-Time PCR System

96 fast- or 384-well plate compatibility (the TaqMan® Low Density Array).7900

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.

External user: 200 sek/plate.

Reservation of Instrument

 

 


 GS Junior System - 454 Sequencing

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

Reservation of Instrument

 


MiSeq Benchtop Sequencer from Illumina (NGS)MiSeq

MiSeq2

 

 

 

 

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.

 

 

Further information: http://www.illumina.com/systems/miseq.ilmn

Reservation of Instrument

External user 600 sek/run

 


 

Agilent Bioanalyzer 2100

Agilent

Users buy their own kits.

Reservation of Instrument

 

 

 

 

 

 


Affymetrix Microarray

Additional Information at www.affymetrix.comAff

DNA:
Do it yourself: 300 sek/chip
External user: 900 sek/chip

EXP:
External user: 600 sek/chip

Reservation of Instrument

Analysis software Array Assist

Reservation of Instrument


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.Fuji

Detection methods:
Fluoroscence
Chemiluminescence
Isotopes

Additional information at www.fujifilm.com/index.html

 

 

 

 


QIAGEN Tissue Lyser

 For high-throughput disruption of a wide range of biological samplesQia
• 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 www.qiagen.com

 


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.

Bokning av instrument

 

 

 

 


Biomek 2000

Biomek 2000 är en pipetteringsrobot för små volymer. Användare kan skriva egna program för roboten. Två åttakanalspipetter finns tillgängliga, 2-20ul samt 5-200ul. Tre singelkanalspipetter finns också, 2-20, 5-200 och 50-1000ul. Roboten kan hantera 96-håls och 384-hålsplattor samt olika provrör. Spetsar köps in individuellt av varje användare.

 

Reservation of Instrument


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.

 

 

 

 

Reservation of Instrument


PyroMark (Klinisk farmakologi, hus 420)

För att köra instrumentet krävs att man genomgår en utbildning för att få körkort på det. En lista på personer som har behörighet att genomföra utbildningen finns vid instrumentet. Kontaktperson: Malin Lindqvist Appell, tel 013-286880, malin.lindqvist.appell@liu.se


PyroMark Q96 MD

Apparat
PyroMark är en realtids sekvenseringsutrustning baserad på pyrosekvensering där 96 prover sekvenseras parallellt. Läslängder omkring 30 - 50 baser från första basen efter sekvenseringsprimer. En klar fördel är att man får ett pyrogram som kvalitetskontroll.

Applikationer:

• SNP
• DNA-metylering
• Sekvensering

Kostnad:
Kontakta Malin Lindqvist Appell för kostnad per körning. Lösningar till preparationsstationen och buffertar ingår. Plaster, reagens och sepharose kulor får användaren själv anskaffa.

Bokning av instrumentet: Bokningslista finns utanför lokalen.


Page manager: mikael.pihl@liu.se
Last updated: Fri Jul 31 12:49:09 CEST 2015