Publication Details

Category Text Publication
Reference Category Journals
DOI 10.1016/j.jbiotec.2014.09.012
Title (Primary) CEM-Designer: design of custom expression microarrays in the post-ENCODE era
Author Arnold, C.; Externbrink, F.; Hackerm├╝ller, J. ORCID logo ; Reiche, K.
Source Titel Journal of Biotechnology
Year 2014
Department PROTEOM
Volume 189
Page From 154
Page To 156
Language englisch
Keywords Transcriptomics; Pervasive transcription; Non-coding RNA; Custom expression microarray; Microarray design
UFZ wide themes RU3;
Abstract Microarrays are widely used in gene expression studies, and custom expression microarrays are popular
to monitor expression changes of a customer-defined set of genes. However, the complexity of transcriptomes
uncovered recently make custom expression microarray design a non-trivial task. Pervasive
transcription and alternative processing of transcripts generate a wealth of interweaved transcripts that
requires well-considered probe design strategies and is largely neglected in existing approaches.

We developed the web server CEM-Designer that facilitates microarray platform independent design
of custom expression microarrays for complex transcriptomes. CEM-Designer covers (i) the collection
and generation of a set of unique target sequences from different sources and (ii) the selection of a set of
sensitive and specific probes that optimally represents the target sequences. Probe design itself is left to
third party software to ensure that probes meet provider-specific constraints.

CEM-Designer is available at
Persistent UFZ Identifier
Arnold, C., Externbrink, F., Hackerm├╝ller, J., Reiche, K. (2014):
CEM-Designer: design of custom expression microarrays in the post-ENCODE era
J. Biotechnol. 189 , 154 - 156 10.1016/j.jbiotec.2014.09.012