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BioMed Research International
Volume 2014, Article ID 857329, 11 pages
Research Article

Differences in Brain Transcriptomes of Closely Related Baikal Coregonid Species

1M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street, 16/10, V-437, 117997 Moscow, Russia
2Limnological Institute, Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia

Received 1 April 2013; Revised 2 October 2013; Accepted 28 October 2013; Published 29 January 2014

Academic Editor: Vassily Lyubetsky

Copyright © 2014 Oksana S. Bychenko et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Supplementary Material

Pairwise Audic and Claverie test are presented. RNA samples were used for cDNA synthesis and production of 21 nt tags. These tags were ligated to form ditags, and then concatemerized and cloned. 250 clones from each SAGE library were sequenced. 1894 and 2670 tags were identified in the whitefish and omul libraries, respectively (see Web Supplementary File Appendix 1). As the sequencing depth was not high enough to cover all transcripts, only the tags originating from the genes with the highest levels of expression were discovered this way.

Table S1: (Web Supplementary File Appendix 1) Complete set of short representative cDNA sequences (tags) extracted from concatamer sequencing data of the SAGE libraries obtained for whitefish and omul brain using RIDGES software. 1894 and 2670 tags were identified in the whitefish and omul libraries, respectively. A total of 2768 of unique tags were extracted and used for identification of differentially expressed genes by IDEG6.

Table S2: (Web Supplementary File Appendix 2) Identification of differentially expressed genes by IDEG6. The pairwise Audic & Claverie test was applied. 36 of 2768 tags were found to be differentially expressed between whitefish and omul, while the differences in the numbers of another 2732 unique tags were too small to be statistically significant.

Table S3: (Web Supplementary File Appendix 3). Comparison of some cDNA fragments (tags) with cDNA sequences of different organisms, annotated in available databases. The results for tags with 70–100% identity level to known genes are presented. We considered as statistically significant differences between whitefish and omul libraries in the range 0.6 > Difwh >1.6 that corresponds to the statistical significance level p>0.999. Difwh is the relative content of a given tag in the whitefish library (relative to omul), Difwh= (Nwh / Nom) х 1.41, Nwh and Nom are the numbers of the given tag in the libraries of Baikal whitefish and omul, respectively, and 1.41 is the correction coefficient equal to the ratio 2670/1894.

  1. Supplementary Materials