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After removing those miRNAs with expression levels that were too low to be analyzed for differential expression, 141 novel miRNAs were identified, of which 77 were differentially expressed; novel262 had the highest abundance with 833 transcripts per million (TPM), followed by novel345 with 43 TPM in the 24 °C library.
Of these, 5015 clones were enriched via the SSH/microarray assays and could be analyzed for differential expression (intensities >500 unit after the noise intensity subtracted).
This resulted in 24 27% (PE) and 26 30% (PF) unambiguous tags per lane to be analyzed for differential expression (Additional file 3).
More genes could be analyzed for differential expression (6,122 genes with the P. fastigiatum reference while only 3,884 genes could be studied with the A. thaliana reference when mapping with no mismatches).
One hundred forty-nine known miRNAs in the two P. pyrifolia libraries were obtained and identified after removing miRNAs in which the expression levels were too low to be analyzed for differential expression (Additional file 3).
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Proteins quantified in at least 3 out of 4 measurements for any growth condition were analyzed for differential expression using the analysis of variance (ANOVA) method with Bonferroni multiple testing correction.
As non-induced HUCPVCs express myogenic markers including desmin, vimentin and alpha smooth muscle actin [37], [38], [39], myogenically-induced cells (Figure 1J,K,P) were analyzed for differential expression of MyoD and fast skeletal myosin light chain (FSMLC).
To determine the impact of the accumulation of DNA repair intermediates on gene expression, the five yeast strains with altered expression of BER repair enzymes were analyzed for differential gene expression.
21,480 transcripts were analyzed for differential expression.
Data generated from gene array were analyzed for differential geneexpression.
The unique best cis-eQTLs were analyzed for differential representation by chromosomes.
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