Geniom® Technology—The Benchtop Array Facility

Güimil, R; Beier, Markus; Scheffler, Matthias; Rebscher, H; Funk, Julie A.; Wixmerten, Anke; Baum, Michaël; Hermann, Corinna; Tahedl, H; Moschel, E; Obermeier, F; Sommer, Iris E.; Buchner, Daniel; Viehweger, R; Burgmaier, J; Stähler, Cord; Müller, Markus; Stähler, Peer F.

doi:10.1081/ncn-120023122

Cited by 7 publications

(3 citation statements)

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“…Oligonucleotide probes were synthesized by light-activated in situ oligonucleotide synthesis inside a Biochip of a Geniom Ò instrument (febit biotech GmbH, Germany) (Guimil et al, 2003). The probe set was calculated from the full genome sequence using proprietary software of febit biotech based on a modified Smith-Waterman algorithm (Smith and Waterman, 1981).…”

Section: Probe and Microarray Designmentioning

confidence: 99%

Gene expression in Fusarium graminearum grown on plant cell wall

Carapito¹,

Hatsch²,

Vorwerk³

et al. 2008

Fungal Genetics and Biology

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Section: Probe and Microarray Designmentioning

confidence: 99%

Gene expression in Fusarium graminearum grown on plant cell wall

Carapito¹,

Hatsch²,

Vorwerk³

et al. 2008

Fungal Genetics and Biology

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“…Total RNA, including miRNAs, was extracted using the miRNeasy Mini Kit (Qiagen GmbH, Hilden, Germany) and stored at -80°C. All samples were analyzed on the automated Geniom Real Time Analyzer (GRTA, febit biomed GmbH, Heidelberg, Germany) using the Geniom miRNA Biochip for Homo sapiens, covering 866 human miRNA species [ 50 ]. Since miRBase has been updated from version 12 to 14 during the time course of the study, we used 863 miRNAs that were consistently present in all three versions for the final data analysis.…”

Section: Methodsmentioning

confidence: 99%

Sparse Modeling Reveals miRNA Signatures for Diagnostics of Inflammatory Bowel Disease

et al. 2015

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The diagnosis of inflammatory bowel disease (IBD) still remains a clinical challenge and the most accurate diagnostic procedure is a combination of clinical tests including invasive endoscopy. In this study we evaluated whether systematic miRNA expression profiling, in conjunction with machine learning techniques, is suitable as a non-invasive test for the major IBD phenotypes (Crohn's disease (CD) and ulcerative colitis (UC)). Based on microarray technology, expression levels of 863 miRNAs were determined for whole blood samples from 40 CD and 36 UC patients and compared to data from 38 healthy controls (HC). To further discriminate between disease-specific and general inflammation we included miRNA expression data from other inflammatory diseases (inflammation controls (IC): 24 chronic obstructive pulmonary disease (COPD), 23 multiple sclerosis, 38 pancreatitis and 45 sarcoidosis cases) as well as 70 healthy controls from previous studies. Classification problems considering 2, 3 or 4 groups were solved using different types of penalized support vector machines (SVMs). The resulting models were assessed regarding sparsity and performance and a subset was selected for further investigation. Measured by the area under the ROC curve (AUC) the corresponding median holdout-validated accuracy was estimated as ranging from 0.75 to 1.00 (including IC) and 0.89 to 0.98 (excluding IC), respectively. In combination, the corresponding models provide tools for the distinction of CD and UC as well as CD, UC and HC with expected classification error rates of 3.1 and 3.3%, respectively. These results were obtained by incorporating not more than 16 distinct miRNAs. Validated target genes of these miRNAs have been previously described as being related to IBD. For others we observed significant enrichment for IBD susceptibility loci identified in earlier GWAS. These results suggest that the proposed miRNA signature is of relevance for the etiology of IBD. Its diagnostic value, however, should be further evaluated in large, independent, clinically well characterized cohorts.

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“…Nucleotide Synthesis Light-activated in situ oligonucleotide synthesis was performed essentially as described by Singh-Gasson et al (Singh-Gasson et al, 1999) using a digital micromirror device (Güimil et al, 2003). The synthesis was performed within the geniom one device (Febit AG, Heidelberg, Germany) on an activated three-dimensional reaction carrier consisting of a glass-silica-glass sandwich (DNA processor).…”

Section: Dna-microarray Production and In Situ Oligomentioning

confidence: 99%

Clustering approach to detect mRNA-degradation patterns from DNA–microarray gene-expression data

Motameny

Wünschiers

2012

BIT-journal

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DNA-microarray based gene-expression analysis is based on hybridization events between messenger RNA (mRNA) and single stranded DNA probes. In oligo nucleotide DNA-microarrays the probes consist of approximately 20 to 80 nucleotides long DNA-molecules. Consequently, several unique probes perfectly matching each single open reading frame (ORF) of mono-or polycistronic mRNA are usually used. If these probes are distributed over the whole length of the mRNA molecule, information about mRNA-degradation patterns can be gathered with data clustering methods. Here we report analysis of expression of 1107 open reading frames from the cyanobacterium Nostoc PCC 7120. Each open reading frame was covered by 10 unique 25 nucleotides long probes and analyzed by 4 independent DNA-microarray experiments. Both the positional information and the absolute expression value for each probe were used to infer clusters of transcripts that show similar expression patterns. Hierarchical and fuzzy k-means clustering yielded comparable results. Our results suggest that several different mRNA-degradation mechanisms, specific for certain transcripts, work in concert.

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Geniom® Technology—The Benchtop Array Facility

Abstract: Febit AG develops an integrated benchtop instrument for in situ microarrays preparation, hybridization, readout and data analysis.

Cited by 7 publications

References 0 publications

Gene expression in Fusarium graminearum grown on plant cell wall

Gene expression in Fusarium graminearum grown on plant cell wall

Sparse Modeling Reveals miRNA Signatures for Diagnostics of Inflammatory Bowel Disease

Clustering approach to detect mRNA-degradation patterns from DNA–microarray gene-expression data

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