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This criterion should be evaluated for a broad range of transcripts.
This in turn provides a broad range of transcripts and pathways that could potentially be modulated by small RNAs, perhaps including siRNAs that function as microRNAs.
The length wise distribution of the unigenes is presented in Additional file 3A, indicating the trancriptome with broad range of transcripts.
A broad range of transcripts indentified in this study were associated with amino acid metabolism and biosynthesis; based on the KEGG databases [ 36], 18 of the 22 amino acid biosynthesis pathways were represented by 100 454 contigs.
For sequencing the whole transcriptome we used RNA samples from nine different conditions (exponential growth phase, heat and cold shock, salt stress, oxidative stresses, and ethanol stress) to obtain a broad range of transcripts.
Furthermore, thanks to the high sequencing depth applied and to the broad range of transcripts expressed, the assembly also contains a great amount of sequence data originated from genes which are not directly linked to liver and testis, permitting to obtain a good overview of the overall coelacanth transcriptome.
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These yielded a broad range of transcript levels, and it was necessary to place some boundaries on what transcript levels can be confidently ascribed to be above background levels.
To explore the broadest range of transcripts, Affymetrix extended probes were imported, yielding transcripts of which 112,207 have annotation with 50,601 at the gene or mRNA-level.
Although this sampling process has been highly effective, a determination of the exact composition of the pea transcriptome will require a corresponding genomic sequence assembly, permitting annotation and classification of a broader range of transcripts.
The two tissues used for the deep RNA-seq of L. menadoensis were both richer than muscle, although testis resulted to be, by far, the one expressing a broader range of transcripts.
Because RNA-Seq detects a broader range of transcripts than microarrays, which are limited to the probe set, any genes not found on the array were first filtered from the RNA-Seq data.
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