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Whereas LocustDB contains EST data derived from primary (i.e. non-normalized) cDNA libraries for head, hind leg, midgut and whole organisms (5th larval stage), the novel S. gregaria database entirely focused on transcript information from the CNS (3 5th larval stage and adults).
Many studies on retrograde signalling from the chloroplast to the nucleus focused on transcript regulation as easy readout and on genetic approaches to identify disturbances.
We note that insertion of the URA3 ORF could affect transcript stability, although the nature of the promoter may be the primary determinant of transcript stability (Bregman et al., 2011; Trcek et al., 2011), so we focused on transcript size and relative abundance.
Through syntenic analysis among 3 species, we focused on transcript expression level of 5 CNL and 16 TNL NBS-encoding genes in different tissues in A. thaliana which have their corresponding orthologous and paralogous genes in B. rapa and B. oleracea genomes to investigate expression pattern divergence among 3 species.
This left us with ∼55 million paired reads that were subjected to de novo assembly using CLC-Bio assembly cell 4. The best results were received using the default parameters; however, we focused on transcript contigs longer than 100 bp in length.
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Therefore, to further identify candidate genes of specific relevance in the regulation of muscle hyperplasia, we focused on transcripts encoding cell-autonomous (intrinsic) factors such as transcriptional regulators and membrane associated proteins, and on transcripts encoding extrinsic factors such as secreted factors, including growth factors and signalling molecules.
To identify RNase L targets we focused on transcripts that were down-regulated upon RNase L induction (Supplemental Table S1).
To extend this analysis, we then focused on transcripts that were at least 4 times over-expressed in either hFL or HEF cells.
To test how gene duplication and associated gene expression variation may shape Arabidopsis metabolism, I focused on transcripts associated with specific metabolic pathways using the AraCyc databases predictions [20], [21].
We focused on transcripts with at least three exons.
We focused on transcripts of adhesion molecules, secreted proteins or molecules displayed on the cell surface.
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