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Transposable elements reveal a stem cell-specific class of long noncoding RNAs

David Kelley123 and John Rinn123*

Author Affiliations

1 Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA

2 Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA

3 Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA

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Genome Biology 2012, 13:R107  doi:10.1186/gb-2012-13-11-r107

Published: 26 November 2012

Additional files

Additional file 1:

Supplementary results and figures. [94]

Format: DOCX Size: 5.8MB Download file

Open Data

Additional file 2:

TE content of lincRNAs. Excel table describing TE content of lincRNAs and statistical analysis.

Format: XLSX Size: 128KB Download file

Open Data

Additional file 3:

TE content of protein coding genes. Excel table describing the TE content of protein coding genes and statistical analysis.

Format: XLSX Size: 127KB Download file

Open Data

Additional file 4:

RNA-Seq data. Excel table describing RNA-Seq datasets used to build lincRNAs and estimate abundances.

Format: XLSX Size: 48KB Download file

Open Data

Additional file 5:

TEs in lincRNAs orientation statistics. Excel table describing orientation statistics of TEs in lincRNAs.

Format: XLSX Size: 106KB Download file

Open Data

Additional file 6:

ChIP-Seq data. Excel table describing ChIP-Seq datasets used to study HERHV-lincRNAs.

Format: XLSX Size: 49KB Download file

Open Data

Additional file 7:

GTF file describing our full lincRNA catalog.

Format: GTF Size: 7.1MB Download file

Open Data

Additional file 8:

GTF file describing only the most expressed isoforms of our lincRNA catalog.

Format: GTF Size: 2.5MB Download file

Open Data

Additional file 9:

Cufflinks output file describing abundance estimates for our full lincRNA catalog.

Format: GZ Size: 8.4MB Download file

Open Data