Open Access Research

Genetic basis of transcriptome differences between the founder strains of the rat HXB/BXH recombinant inbred panel

Marieke Simonis1, Santosh S Atanur2, Sam Linsen1, Victor Guryev1, Frans-Paul Ruzius1, Laurence Game3, Nico Lansu1, Ewart de Bruijn1, Sebastiaan van Heesch1, Steven JM Jones4, Michal Pravenec5, Tim J Aitman2* and Edwin Cuppen1*

Author Affiliations

1 Genome Biology Group, Hubrecht Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands

2 Physiological Genomic and Medicine Group, Medical Research Councils Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital, London W12 ONN, UK

3 Genomics Laboratory, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital, London W12 ONN, UK

4 Genome Sciences Centre, BC Cancer Agency, Suite 100 570 West 7th Avenue, Vancouver, British Columbia, Canada V5Z 4S6

5 Institute of Physiology, Academy of Sciences of the Czech Republic, Videnska 1083, 14220 Prague 4, Czech Republic

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Genome Biology 2012, 13:r31  doi:10.1186/gb-2012-13-4-r31

Published: 27 April 2012

Additional files

Additional file 1:

Summary of genomic sequencing data. A table listing the genomic sequencing data.

Format: PDF Size: 268KB Download file

This file can be viewed with: Adobe Acrobat Reader

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Additional file 2:

SNVs in SHR. List of all SNVs found in the SHR strain.

Format: GZ Size: 12.6MB Download file

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Additional file 3:

SNVs in BN-Lx. List of all SNVs found in the BN-Lx strain.

Format: GZ Size: 68KB Download file

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Additional file 4:

Validation of SNVs. A table containing the details on the validated SNVs.

Format: XLS Size: 25KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 5:

Supplementary figures S1, S2 and S3.

Format: PDF Size: 920KB Download file

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Additional file 6:

Indels in SHR. List of all indels found in the SHR strain.

Format: GZ Size: 2.4MB Download file

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Additional file 7:

Indels in BN-Lx. List of all indels found in the BN-Lx strain.

Format: GZ Size: 10KB Download file

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Additional file 8:

Validation of indels. A table that contains the details on the validated indels.

Format: XLS Size: 23KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 9:

Structural variants. A list of all the SVs found in SHR and BN-Lx.

Format: XLS Size: 183KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 10:

Splice-site differences between BN-Lx and SHR. A table listing splice sites that were found to be differentially used in SHR versus BN-Lx.

Format: PDF Size: 568KB Download file

This file can be viewed with: Adobe Acrobat Reader

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Additional file 11:

Genes with stop codon and splice-site SNVs. A table listing genes that contain SNVs in stop codons or essential splice sites.

Format: XLS Size: 46KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 12:

Genes with stop codon or frameshift indels. A table listing genes that contain indels that are located in stop codons or that cause frameshifts.

Format: XLS Size: 56KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 13:

Genes with SVs. A table listing genes that overlap SVs.

Format: XLS Size: 920KB Download file

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Additional file 14:

Validation of stop codon SNVs. A table that contains the details on the validation of the SNVs that are predicted to create new stop codons.

Format: XLS Size: 16KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data