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Whole transcriptome analyses of six thoroughbred horses before and after exercise using RNA-Seq

Kyung-Do Park1, Jongsun Park2, Junsu Ko3, Byung Chul Kim23, Heui-Soo Kim4, Kung Ahn4, Kyoung-Tag Do5, Hansol Choi2, Hak-Min Kim2, Sanghoon Song3, Sunghoon Lee2, Sungwoong Jho2, Hong-Sik Kong1, Young Mok Yang6, Byung-Hak Jhun7, Chulhong Kim3, Tae-Hyung Kim3, Seungwoo Hwang8, Jong Bhak23*, Hak-Kyo Lee1* and Byung-Wook Cho5*

Author Affiliations

1 Department of Biotechnology, Hankyong National University, Anseong, 456-749, Republic of Korea

2 Personal Genomics Institute, Genome Research Foundation, 443-270, Suwon, Republic of Korea

3 Theragen BiO Institute, TheragenEtex, 443-270, Suwon, Republic of Korea

4 Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan, 609-735, Republic of Korea

5 Department of Animal Science, College of Life Sciences, Pusan National University, Miryang, 627-702, Republic of Korea

6 Department of Pathology, School of Medicine, and Institute of Biomedical Science and Technology, Konkuk University, Seoul, 143-701, Republic of Korea

7 Department of Nanomedical Engineering, College of Nanoscience and Nanotechnology, Pusan National University, Miryang, 627-702, Republic of Korea

8 Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, 305-806, Daejeon, Republic of Korea

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BMC Genomics 2012, 13:473  doi:10.1186/1471-2164-13-473

Published: 12 September 2012

Additional files

Additional file 1:

Figure S1. Six thoroughbred horses. Table S1. 24 sample names from six thoroughbred horses used in this study. Table S2. The statistics of RNA-Seq raw data from 24 different samples. Table S3. The mapping results against the horse reference genome (Ensembl 62). Figure S2. Procedure for identifying horse unigenes. Figure S3. Distribution plot of the exons identified without gene models which contain ORFs. Figure S4. Reverse transcript PCR (RT-PCR) confirmation of the 8 novel unigene clusters (UCs) Table S4. Primer information for the RT-PCR experiment. Table S5. Statistics of the filtered de novo transcripts identified from cufflink. Table S6.de novo assembly results from one sample with various k-mer values. Table S7.de novo assembly of unmapped sequences originated from 24 samples. Table S8. Filtered and clustered unigenes from the scaffolds assembled from unmatched sequences. Figure S5. The whole process of identifying SNVs. Table S9. The proportion of the scaffolds from the unmapped sequences which were matched against the human genome. Table S10. The statistics of total SNVs identified from 24 samples. Table S11. The number of total SNVs identified in thoroughbred horses. Table S12. The number of individual-specific SNVs. Table S13. Conformation of the SNPs identified from the mouse sample [2]. Table S14. Distribution of SNP locations in three datasets. Table S15. The list of transcripts which have ten or more non-synonymous SNPs. Figure S6. GO classification of all expressed genes in human, mouse, and horse muscle tissue. Figure S7. GO classification of all expressed horse genes in blood and muscle tissue. Figure S8. Correlation matrix of the 24 samples. Figure S9. Correlation matrix of three human samples from kidney and liver tissues. Figure S10. Histogram of average expression level of the unigene clusters in the 24 samples. Table S16. List of DEGs in muscle and blood tissues. Table S17. Expression profiles of known exercise-related horse genes. Table S18. Comparison between DEGs in muscle tissue and the DEGs which are responsible to exercise training [25]. Table S19. List of transcription factors differentially expressed in muscle and blood tissues. Table S20. RT-PCR primers for seven transcription factors. Table S21. RT-PCR results of differentially expressed transcription factors in muscle tissue. Table S22. The list of four genes of which alternative splicing forms showed reversed expression patterns before and after exercising. Figure S11. Expression profiles of the genes of which alternative splicing forms showed reversed expression patterns before and after exercising. Table S23. Number of filtered de novo transcripts identified by Cufflink. Supplementary methods.

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