Research
Cell-specific microarray profiling experiments reveal a comprehensive picture of gene expression in the C. elegans nervous system
- † Equal contributors
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
Genome Biology 2007, 8:R135 doi:10.1186/gb-2007-8-7-r135
Published: 5 July 2007Additional 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
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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
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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].
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Additional data file 6:
Fifty top-ranked muscle enriched genes.
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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.
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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.
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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.
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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.
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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
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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
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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.
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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.
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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.
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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.
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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
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
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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
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Additional data file 28:
RMA intensities for the embryonic pan-neural (EP) and embryonic reference (ER) datasets.
Format: XLS Size: 4.3MB Download file
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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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