CBS >> CBS Data Sets >> Probe design related data

Thermodynamic probe intensity correction for oligonucleotide microarrays
Georg M. Bruun , Rasmus Wernersson, Agnieszka S. Juncker , Hanni Willenbrock and Henrik Bjørn Nielsen
Nucleic Acids Res. 2007 (Mar 2)

Array design:
Excel-file describing the naming convension and the selection criteria used in OligoWiz 2: NimbleGenArray_final.xls
Cross-reference table mapping descriptive names to the CDF probe names: sc_probes.x-ref.tab
CDF-file: RWSCER01a530205N

Raw data:
CEL-file: CCY-15_T030.CEL

Processed data:
Combined information (probeid, probe description, DNA sequence, DNA annotation, raw intensity, corrected intensity): Bruun.suppl.data.tab

Software implementation:
TAR archive containing a C implementation of the model: PD_final.tgz (For UNIX like systems). Please see the "README" file for further instructions.

An implementation as an R package is currently being developed.

Probe selection for DNA microarrays using OligoWiz
Rasmus Wernersson, Agnieszka S Juncker and Henrik Bjørn Nielsen
Nature Protocols (2007) vol. 2, no. 11, p. 2677-91

OligoWiz 2.0 - integrating sequence feature annotation into design of microarray probes
Rasmus Wernersson and Henrik Bjørn Nielsen.
Nucleic Acids Research, 2005, Vol. 33, Web Server issue W611-W615
Web: http://www.cbs.dtu.dk/services/OligoWiz2/

Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays.
Henrik Bjørn Nielsen, Rasmus Wernersson and Steen Knudsen.
Nucleic Acids Research, 2003, Vol. 31, No. 13 3491-3496
Web: http://www.cbs.dtu.dk/services/OligoWiz/