Research
High resolution transcriptome maps for wild-type and nonsense-mediated decay-defective Caenorhabditis elegans
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* Corresponding authors: Thomas R Gingeras gingeras@cshl.edu - Andrew G Fraser andyfraser.utoronto@gmail.com
- † Equal contributors
1 Donnelly CCBR, College Street, University of Toronto, Toronto, M5S 3E1, Canada
2 The Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
3 Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3DY, UK
4 Affymetrix, Inc., Central Expressway, Santa Clara, CA 95051, USA
5 Helicos Biosciences Corporation, Cambridge, MA 02139, USA
6 Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY 11724, USA
Genome Biology 2009, 10:R101 doi:10.1186/gb-2009-10-9-r101
Published: 24 September 2009Additional files
Additional data file 1:
Table S1 shows the number of genes identified as expressed at each stage in wild-type (N2) and smg-1(r861) worms. Table S2 shows the transfrag distribution at each developmental stage. Table S3 shows numbers of reads from sequencing and mapping statistics. Table S4 shows the number of tiling array transfrags confirmed by sequencing. Table S5 shows the overlap of genes detected between our data and that from Hillier et al. [17]. Table S6 shows the number of transfrags identified using tiling data, and the number of these also detected by either our sequence data or the Hillier et al. sequence data. Table S7 indicates the average ratio of expression for the families of splicing factors between the mutant and wild type at each of the time points based on both tiling and sequencing. Table S8 shows the list of 132 hand-curated splice factors.
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Additional data file 2:
Distribution of mapped sequence reads.
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Additional data file 3:
This figure is analogous to Figure 1 for N2 (wild type).
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Additional data file 4:
For each gene the length of the 3' UTR (if greater than average), occurrence of uORFs and the presence of introns that are expressed in the mutant are listed.
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Additional data file 5:
Structural changes in SR gene transcripts between N2 and smg-1(r861).
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Additional data file 6:
Each sequence was created by combining 33 nucleotides from the 3' end of the upstream exon with 33 nucleotides from the 5' end of the downstream exon using the WS150 release of the Wormbase gene models.
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