Open Access Research article

Deciphering the porcine intestinal microRNA transcriptome

Soroush Sharbati1*, Marc R Friedländer2, Jutta Sharbati1, Lena Hoeke1, Wei Chen23, Andreas Keller4, Peer F Stähler4, Nikolaus Rajewsky2 and Ralf Einspanier1

Author Affiliations

1 Freie Universität Berlin, Institute of Veterinary Biochemistry, Oertzenweg 19b, 14163 Berlin, Germany

2 Max Delbrück Centrum für Molekulare Medizin, Robert-Rössle-Strasse 10, 13125 Berlin, Germany

3 Max Planck Institute for Molecular Genetics, Department of Human Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany

4 febit biomed gmbh, Im Neuenheimer Feld 519, 69120 Heidelberg, Germany

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BMC Genomics 2010, 11:275  doi:10.1186/1471-2164-11-275

Published: 30 April 2010

Additional files

Additional file 1:

Identified porcine miRNAs by miRDeep. Hairpin forming precursors and mature porcine miRNAs were identified from deep sequencing data using the miRDeep algorithm. The table consists of 399 miRDeep scored molecules including assigned porcine miRNAs.

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Additional file 2:

Identified conserved porcine mature miRNAs by homology search. Mature porcine miRNAs were identified from deep sequencing data by performing a search for conserved miRNAs among the sequencing reads.

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Additional file 3:

List of validated novel porcine miRNAs by means of customized microarrays or homology search. 201 apparently novel porcine miRNAs out of 399 miRDeep predicted sequences were identified either by means of microarray or by homology search.

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Additional file 4:

miRNAome of the entire porcine intestine identified by means of customized Microarrays. Background subtracted and variance stabilization normalized (VSN) signal intensities of all samples (duodenum, proximal and distal jejunum, ileum, ascending and transverse colon as well as the common reference) is shown as tab delimited text file.

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