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Cell-specific microarray profiling experiments reveal a comprehensive picture of gene expression in the C. elegans nervous system

Stephen E Von Stetina1, Joseph D Watson2, Rebecca M Fox13, Kellen L Olszewski14, W Clay Spencer1, Peter J Roy5 and David M Miller12*

Author Affiliations

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

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

3 Department of Cell Biology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA

4 Department of Molecular Biology, Lewis-Sigler Institute for Integrative Genomics, Princeton University 246 Carl Icahn Laboratory, Princeton NJ 08544, USA

5 Department of Medical Genetics and Microbiology, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 1A, Canada

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Genome Biology 2007, 8:R135  doi:10.1186/gb-2007-8-7-r135

Published: 5 July 2007

Additional files

Additional data file 1:

Enriched genes from the larval pan-neural (LP), embryonic pan-neural (EP), larval A-class (LA), and embryonic A-class (EA) microarray datasets.

Format: XLS Size: 2.6MB Download file

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Additional data file 2:

Master annotation file of all spots on the C. elegans Affymetrix microarray (based on WormBase releases WS140 and WS146).

Format: XLS Size: 10MB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional data file 3:

Master annotation file of all genes represented on the C. elegans Affymetrix microarray (based on WormBase releases WS140 and WS146).

Format: XLS Size: 9.9MB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional data file 4:

Larval pan-neural (LP), embryonic pan-neural (EP), larval A-class (LA), and embryonic A-class (EA) enriched datasets categorized into gene families.

Format: XLS Size: 1011KB Download file

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Additional data file 5:

Comparison of the larval pan-neural (LP) and larval A-class (LA) enriched transcripts to the 1,926 GMI enriched genes found on the C. elegans Affymetrix chip [13].

Format: XLS Size: 3.1MB Download file

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Additional data file 6:

Fifty top-ranked muscle enriched genes.

Format: XLS Size: 54KB Download file

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Additional data file 7:

Larval pan-neural enriched genes with known expression patterns from Figure 3b.

Format: XLS Size: 147KB Download file

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Additional data file 8:

Representative scatter plots and R2 values for pairwise combinations of the embryonic pan-neural (EP) and larval A-class (LA) datasets.

Format: PPT Size: 480KB Download file

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Additional data file 9:

Twenty-seven uncharacterized human homologues in the larval pan-neural (LP) and embryonic pan-neural (EP) datasets, and mouse homologs and expression in mouse brain.

Format: XLS Size: 23KB Download file

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Additional data file 10:

Comparisons of all enriched datasets (larval pan-neural (LP) versus embryonic pan-neural (EP); LP versus larval A-class (LA); EP versus embryonic A-class (EA); LA versus EA) shown in Figure 8.

Format: XLS Size: 3.1MB Download file

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Additional data file 11:

Comparisons of all enriched datasets versus a MAPCeL profile of chemosensory neurons (AFD/AWB) [8] shown in Figure 8.

Format: XLS Size: 2.2MB Download file

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Additional data file 12:

EGs from the embryonic pan-neural (EP), embryonic A-class (EA), and embryonic reference (ER) datasets.

Format: XLS Size: 9.6MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional data file 13:

EGs from the larval pan-neural (LP), larval A-class (LA), and larval reference (LR) datasets.

Format: XLS Size: 7.3MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional data file 14:

11,868 unique transcripts identified by all of our microarray experiments.

Format: XLS Size: 7.8MB Download file

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Additional data file 15:

Comparison of the GMIc dataset to the larval pan-neural (LP) EG and larval reference (LR) EG datasets.

Format: XLS Size: 7.5MB Download file

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Additional data file 16:

The approximately 1,600 EGs without EST confirmation plus a subset enriched in the larval pan-neural (LP), embryonic pan-neural (EP), embryonic A-class (EA), and larval A-class (LA) neural datasets.

Format: XLS Size: 617KB Download file

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Additional data file 17:

Complete list of GFP expression patterns.

Format: PDF Size: 92KB Download file

This file can be viewed with: Adobe Acrobat Reader

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Additional data file 18:

Description of the dauer pathway genes identified in our larval pan-neural (LP) and embryonic pan-neural (EP) enriched datasets.

Format: XLS Size: 80KB Download file

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Additional data file 19:

The 162 common A-class enriched genes categorized into gene families.

Format: XLS Size: 43KB Download file

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Additional data file 20:

mRNA-tagging bench protocol.

Format: DOC Size: 813KB Download file

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Additional data file 21:

The RMA normalized intensity values for these genes, plus those from the larval reference (LR) dataset, are included.

Format: XLS Size: 7.6MB Download file

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Additional data file 22:

Perl script used to search WormBase expression data (keyword_search.pl).

Format: PL Size: 5KB Download file

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Additional data file 23:

Keywords used to search WormBase expression data.

Format: XLS Size: 15KB Download file

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Additional data file 24:

Enriched genes from all datasets with uncharacterized human homologues.

Format: XLS Size: 82KB Download file

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Additional data file 25:

MAS5.0 intensities for the embryonic pan-neural (EP), larval pan-neural (LP), and larval A-class (LA) datasets.

Format: XLS Size: 9.8MB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional data file 26:

MAS5.0 intensities for the larval reference (LR) dataset.

Format: XLS Size: 4.6MB Download file

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Additional data file 27:

RMA intensities for the larval pan-neural (LP), larval A-class (LA), and larval reference (LR) datasets.

Format: XLS Size: 9.3MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional data file 28:

RMA intensities for the embryonic pan-neural (EP) and embryonic reference (ER) datasets.

Format: XLS Size: 4.3MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional data file 29:

Comparison of the embryonic and larval pan-neural enriched datasets to the list of candidate neural genes containing a presumptive pan-neural cis-regulatory element [48].

Format: XLS Size: 371KB Download file

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Open Data