Open Access Research article

Establishing the baseline level of repetitive element expression in the human cortex

Svitlana Tyekucheva12, Robert H Yolken3, W Richard McCombie4, Jennifer Parla4, Melissa Kramer4, Sarah J Wheelan567* and Sarven Sabunciyan3*

Author Affiliations

1 Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, 02115, USA

2 Department of Biostatistics, Harvard School of Public Health, 677 Huntington Ave, Boston, 02115, USA

3 Department of Pediatrics, Johns Hopkins University School of Medicine, 600 N. Wolfe Street, Baltimore, 21287, USA

4 Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, 11724, USA

5 Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, 550 N. Broadway, Baltimore, 21205, USA

6 Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, 21205, USA

7 Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, 21205, USA

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BMC Genomics 2011, 12:495  doi:10.1186/1471-2164-12-495

Published: 10 October 2011

Additional files

Additional file 1:

Summary of Alignment Results. Results from aligning each sample to the human genome (build hg18), CCDS database, repeats database, repeat masked intronic and repeat masked intergenic regions.

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Additional file 2:

The 5 prime end of the L1 element is overrepresented in the sequencing reads (in comparison with the simulated reads). Full length L1 elements appear to be expressed at proportions much higher than expected based on the fraction of the genome they compose. For this figure we realigned the reads (both observed and simulated), which mapped to L1s from our repeats database, to the collection of consensus sequences of full length active copies of the L1 elements. We used the LASTZ alignment program [33]http://www.bx.psu.edu/~rsharris/lastz/ webcite instead of Bowtie for this task. Each of the aligning reads usually mapped to several consensus sequences (because they are similar), so we calculated an average base on the L1 where the alignment started. In this plot we show a representative histogram of the distribution of these average starting points for one of the samples and a single draw of simulated reads.

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