Complementary RNA amplification methods enhance microarray identification of transcripts expressed in the C. elegans nervous system

doi:10.1186/1471-2164-9-84

BMC Genomics

Volume 9

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Watson JD
Wang S
Von Stetina SE
Spencer WC
Levy S
Dexheimer PJ
Kurn N
Heath JD
Miller DM

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Von Stetina SE
Spencer WC
Levy S
Dexheimer PJ
Kurn N
Heath JD
Miller DM
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Methodology article

Complementary RNA amplification methods enhance microarray identification of transcripts expressed in the C. elegans nervous system

Joseph D Watson¹^,2 , Shenglong Wang³ , Stephen E Von Stetina¹ , W Clay Spencer¹ , Shawn Levy⁴ , Phillip J Dexheimer⁴ , Nurith Kurn³ , Joe Don Heath³ and David M Miller III¹^,2

¹Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232-8240, USA

²Graduate Program in Neuroscience, Center for Molecular Neuroscience, Vanderbilt University, Nashville, TN 37232-8548, USA

³NuGEN Technologies, Inc., San Carlos, CA 94070, USA

⁴Department of Biomedical Informatics, Vanderbilt University, Nashville, TN 37232-8240, USA

author email corresponding author email

BMC Genomics 2008, 9:84doi:10.1186/1471-2164-9-84


Published:	19 February 2008

Additional files

Additional File 1:

Genes detected in neurons by WT-Pico and IVT. A list of genes present in 3 of 3 IVT pan-neural samples and 5 of 5 WT-Pico pan-neural samples. Worksheets include genes found multiple times in a single data set (with dups) and a list in which these duplications have been removed (without dups).

Format: XLS Size: 9MB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional File 2:

WT-Pico pan-neural enriched and depleted genes. These worksheets list the pan-neural enriched genes from WT-Pico and also genes depleted in the WT-Pico data set relative to reference samples.

Format: XLS Size: 4.7MB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional File 3:

IVT pan-neural enriched genes. These worksheets contain pan-neural enriched data sets previously published in our lab [8]. This data has been updated from WS140 to WS170 to reflect changes in C. elegans annotation.

Format: XLS Size: 2.5MB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional File 4:

WormBase 170 (WS170) annotated Affymetrix data. This file contains descriptions of all genes on the Affymetrix C. elegans expression array.

Format: XLS Size: 9.1MB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional File 5:

Fold change of transcripts present in both WT-Pico and IVT pan-neural data sets. This file identifies all transcripts present in both IVT and WT-Pico pan-neural data sets and also lists the fold change of these transcripts. This list was used to generate the scatter plot from fig. 5.

Format: XLS Size: 766KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional File 6:

A comparison of transcripts enriched in IVT and WT-Pico pan-neural data sets. The three worksheets contained in this file list genes found in the IVT-only data set, the WT-Pico-only data set, or genes enriched in both the IVT and WT-Pico data sets.

Format: XLS Size: 2.8MB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional File 7:

Uncharacterized conserved genes found in the WT-Pico-only data set. This file contains a list of WT-Pico-only conserved, uncharacterized genes that have available mouse in situ data.

Format: XLS Size: 49KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional File 8:

3' bias analysis of IVT and WT-Pico data. This file contains raw data and charts used to examine 3' bias in IVT and WT-Pico amplifications.

Format: XLS Size: 452KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional File 9:

Full list of GFP reporter lines generated for figure 8. List strain names and full expression patterns of GFP reporter lines built for this analysis.

Format: XLS Size: 16KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional File 10:

Present calls perl script. Perl script file used to determine which genes on the Affymetrix array were present in 3 of 3 IVT samples.

Format: PL Size: 1KB Download file