Open Access Research article

Genetic and epigenetic variations contributed by Alu retrotransposition

Alexandre de Andrade1, Min Wang12, Maria F Bonaldo12, Hehuang Xie12* and Marcelo B Soares12*

Author Affiliations

1 Falk Brain Tumor Center, Cancer Biology and Epigenomics Program, Children's Memorial Research Center, Chicago IL 60614-3394, USA

2 Department of Pediatrics; Feinberg School of Medicine, Northwestern University, Chicago IL 60614-3394, USA

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BMC Genomics 2011, 12:617  doi:10.1186/1471-2164-12-617

Published: 20 December 2011

Additional files

Additional file 1:

Table S1. Putatively recent Alu insertions. Alu insertions identified in eight Alu bisulfite PCR libraries.

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Additional file 2:

Table S2. Clusters of putative Alu insertions. Alu insertions and their gene annotation.

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Additional file 3:

Figure S1. Methylation pattern of recent Alu insertions. To determine the methylation status, the sequences corresponding to the first half of Alu elements plus its 5' flanking regions [31,32] were aligned to the Alu element sequences generated in this study. NC1: Normal cerebellum and NC2: normal 4th ventricle lining tissue; PA1, PA2, PA3, PA4, and PA5: primary ependymoma tumor; RL: ependymoma tumor relapsed from PA3.

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Additional file 4:

Table S3. Alu methylation level. Methylation levels of mapped and 19 non-mapped Alu elements.

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Additional file 5:

Table S4. Validation of identified Alu elements. Primers designed for Alu elements validation.

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