Open Access Highly Accessed Research article

The majority of total nuclear-encoded non-ribosomal RNA in a human cell is 'dark matter' un-annotated RNA

Philipp Kapranov1*, Georges St Laurent28, Tal Raz1, Fatih Ozsolak1, C Patrick Reynolds3, Poul HB Sorensen4, Gregory Reaman5, Patrice Milos1, Robert J Arceci6, John F Thompson1* and Timothy J Triche7*

Author Affiliations

1 Helicos BioSciences Corporation, One Kendall Square, Building 700, Cambridge, MA 02139, USA

2 Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, SFH Life Sciences Building, 185 Meeting St, Providence, RI 02912, USA

3 Cancer Center, Departments of Cell Biology & Biochemistry, Pediatrics, and Internal Medicine, School of Medicine, Texas Tech University Health Sciences Center, 3601 4th Street STOP 9445, Lubbock, TX 79430-6450, USA

4 British Columbia Cancer Research Centre, 675 West 10th Avenue, Room 4112, Vancouver, BC, Canada V5Z 1L3

5 Department of Pediatrics, The George Washington University School of Medicine and Health Sciences, Division of Oncology, Children's National Medical Center, 11 Michigan Ave, NW, Washington, DC, 20422, USA

6 Kimmel Comprehensive Cancer Center at John Hopkins, Department of Oncology/Pediatric Oncology, The Buntings Blaustein Cancer Research Building, 1650 Orleans Street, Suite 207, Baltimore, MD, 21287, USA

7 Department of Pathology, University of Southern California, 1975 Zonal Avenue, Los Angeles, CA 90089-9034, USA

8 Grupo de Inmunovirologia, SIU, Universidad de Antioquia, Calle 67 Número 53 - 108, Medellin, Antioquia, Colombia

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BMC Biology 2010, 8:149  doi:10.1186/1741-7007-8-149

Published: 21 December 2010

Additional files

Additional File 1:

Definition of the 'dark matter' RNA. Provides a definition of what kind of RNA molecules should be included in the 'dark matter' RNA realm and argumentation for their inclusion.

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Additional File 2:

Table S1. Distribution of single-molecule sequencing reads obtained from polyA+, rRNA-depleted (Ribominus) and total RNA from different tissues among different types of annotations.

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Additional File 3:

Table S2. Distribution of single-molecule sequencing reads obtained from ribosomal RNA-depleted (Ribominus) RNA from Ewing Family of Tumours solid tumours and cell lines.

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Additional File 4:

Table S3. Coordinates of the very long intergenic regions and their normalized expression levels in each tissue.

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Additional File 5:

Table S4. Normalized expression levels of University of California Santa Cruz genes in each tissue. The total number of reads within each of the regions was normalized to 10 M non-ribosomal non-mitochondrial unique reads in each sample.

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Additional File 6:

Table S5. Spearman correlation matrix based on expression of very long intergenic non-codings and University of California Santa Cruz genes between different tumour and normal tissues

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Additional File 7:

Table S6. Overlap between very long intergenic non-codings and FANTOM3 intergenic clusters of over 50 kb.

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