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Dynamic expression of small non-coding RNAs, including novel microRNAs and piRNAs/21U-RNAs, during Caenorhabditis elegans development

Masaomi Kato, Alexandre de Lencastre, Zachary Pincus and Frank J Slack*

Author Affiliations

Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA

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Genome Biology 2009, 10:R54  doi:10.1186/gb-2009-10-5-r54

Published: 21 May 2009

Additional files

Additional data file 1:

The number of each RNA species that satisfies the following conditions was counted after searching by the BLASTN program in the pool of sequence reads that aligned to the C. elegans genome; the length of the query is equal to that of the match and the percentage of identical bases in the match is 100%.

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Additional data file 2:

Raw data showing the number of miRNA reads in each developmental stage of hermaphrodites and in young adult males.

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Additional data file 3:

The SOAP-processed aligned reads were searched against miRNA hairpin sequences. Each number represents the total number of reads detected in all developmental stages of hermaphrodites and young adult males. Annotated mature miRNAs are marked with a hatch mark and highlighted in red, and annotated novel miRNAs we report here are colored in green.

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Additional data file 4:

The names of miRNAs with more than a fivefold difference in the number of reads at some point during development and/or between genders are labeled in red and their numbers of reads are compared. The miRNAs with lower numbers of reads (less than ten in the sum of reads in any two stages compared) were not highlighted since their significant changes are not clear due to extremely low reads.

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Additional data file 5:

Vertical axis indicates the relative expression level. The data from both RT-PCR and Solexa sequencing were standardized to the expression level in the embryonic sample as 1. The results were further confirmed using independently prepared RNAs.

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Additional data file 6:

(a) The correlation diagram of all known miRNAs between males and hermaphrodites. (b) The correlation diagram of miRNAs with relatively low abundance (less than 20 × 104 reads in males, yellow-colored area in (a)). (c) Correlation diagram of miRNAs with lower abundance ((less than 10 × 103 reads in males, red-colored area in (a)).

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Additional data file 7:

The numbers of reads were obtained from all developmental stages of hermaphrodites and young adult males. The bona fide novel RNAs with transcripts from their 'star sequence' are highlighted in red. 'Genomically clustered' is defined here as localization within 1.0 kb on the same chromosome.

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Additional data file 8:

Data were normalized by the total number of reads that matched to the C. elegans genome. The miRNAs and their number of reads were highlighted in red as mentioned in the legend for Additional data file 4.

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Additional data file 9:

21U-RNAs in which we found larger transcripts and overlapping ones within 10 bp of other 21U-RNAs, including novel ones we found, are marked with an asterisk and a dagger, respectively.

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Additional data file 10:

The presence of the core consensus motif CTGTTTCA was examined in their possible larger motif regions (-20 to -63 bp upstream of the 5' terminus of each 21nt-U-RNA). This list also contains the novel 21U-RNAs shown in Additional data file 11.

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Additional data file 11:

A larger motif of novel 21U-RNAs represents the region -20 to -63 bp upstream of the 5' terminus of each novel 21U-RNA. 21U-RNAs in which we found larger transcripts and overlapping ones within 10 bp of other 21U-RNAs are marked with an asterisk and a dagger, respectively.

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Additional data file 12:

(a) Number of novel 21U-RNA reads was plotted after normalizing. (b) Total number of reads shown in (a) that mapped on chromosome IV.

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Additional data file 13:

The number of reads was obtained from computational output of the SOAP program followed by removal of redundant sequences, and samples of all six developmental stages (embryo to young adult of hermaphrodites) were used as the input. The sequences of longer transcripts, their nucleotide lengths and the number of reads are highlighted in red.

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