Open Access Highly Accessed Research article

Microarray and cDNA sequence analysis of transcription during nerve-dependent limb regeneration

James R Monaghan1, Leonard G Epp2, Srikrishna Putta1, Robert B Page1, John A Walker1, Chris K Beachy3, Wei Zhu4, Gerald M Pao4, Inder M Verma4, Tony Hunter4, Susan V Bryant56, David M Gardiner56, Tim T Harkins7 and S Randal Voss1*

Author Affiliations

1 Department of Biology and Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, KY 40506, USA

2 Department of Biology, Mount Union College, Alliance, OH 44601, USA

3 Department of Biology, Minot State University, Minot, SD, USA

4 The Salk Institute for Biological Studies, La Jolla, CA 92037, USA

5 Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA 92697, USA

6 The Developmental Biology Center, University of California Irvine, Irvine, CA 92697, USA

7 Roche Applied Science, Indianapolis, IN 46250, USA

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BMC Biology 2009, 7:1  doi:10.1186/1741-7007-7-1

Published: 13 January 2009

Additional files

Additional file 1:

371 unique probe sets upregulated from baseline (D0). The data show all the significant genes identified as upregulated from baseline. The blank cells represent insignificant results at particular time points. Gene functions were hand-annotated using gene ontology terminology, NCBI Entrez Gene descriptions, and Pubmed searches.

Format: XLS Size: 84KB Download file

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Additional file 2:

336 unique probe sets that were downregulated from baseline (D0). The data show all the significant genes identified as downregulated from baseline. The blank cells represent insignificant results at particular time points. Gene functions were hand-annotated using GO terminology, NCBI Entrez Gene descriptions, and Pubmed searches.

Format: XLS Size: 79KB Download file

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Additional file 3:

33 unique probe sets that were significantly different between NR5 and DL5. The data shows the genes that were identified as differentially expressed between NR5 and DL5 limbs. Blank cells represent insignificant results at particular time points. Gene functions were hand-annotated using GO terminology, NCBI Entrez Gene descriptions, and Pubmed searches.

Format: XLS Size: 30KB Download file

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Additional file 4:

282 unique probe sets that were significantly different between NR14 and DL14. The data shows the genes that were identified as differentially expressed between NR14 and DL14 limbs. Blank cells represent insignificant results at particular time points. Gene functions were hand-annotated using GO terminology, NCBI Entrez Gene descriptions, and Pubmed searches.

Format: XLS Size: 68KB Download file

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Additional file 5:

1150 contigs that differed significantly in abundance between cDNA libraries according to 454 sequencing. The data show the normalized counts for genes that were identified as differentially expressed between any of the five libraries. Genes with significant human hits were hand-annotated using GO terminology, NCBI Entrez Gene descriptions, and Pubmed searches.

Format: XLS Size: 2MB Download file

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Additional file 6:

104 genes that were represented on both platforms and found to be differentially expressed according to both microarry and 454 sequencing. The data show the normalized counts for genes identified using 454 sequencing and fold changes for genes identified using microarray analysis. Gene functions were hand-annotated using GO terminology, NCBI Entrez Gene descriptions, and Pubmed searches.

Format: XLS Size: 67KB Download file

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Additional file 7:

Lowly-expressed develeopmental genes from D14 limbs. Important developmental genes that yielded weak, but significant hybridization signals between NR14 and DL14 limbs.

Format: XLS Size: 20KB Download file

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