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We exposed HeLa cells to CHX under hypoxic conditions in the presence or absence of TPZ at different time points and estimated the expression levels of HIF-1α.
We estimated the expression levels of NFκB and IκBα using western blotting.
Hence, we estimated the expression levels of HSP47 following incubation with the cocktail.
When we estimated the expression levels after infection at each separate time point, similar results were observed (Additional file 1: Table S5).
Following that, we estimated the expression levels with their respective uncertainties of each transcript in our C57Bl/6J, Cast/EiJ diploid transcriptome using MMSEQ (Turro et al., 2011).
The positive correlation on a linear regression model between qRT-PCR and RPK values and the high R-squared value demonstrated that RNA-Seq data properly estimated the expression levels of the selected genes.
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We estimated the expression level of each contig by counting 454 reads mapped back to the BT_transcriptome_v2 dataset.
For each mapped RNA-seq library, we then estimated the expression level of each transcript with its respective error, for each allele in a Cast/EiJ×C57Bl/6J diploid transcriptome using MMSEQ (Turro et al., 2011).
Moreover, IDBA-Tran had similar performance to CEM in estimating the expression levels because it could reconstruct most of the expressed transcripts making the estimation process easier.
Since IDBA-Tran is designed for assembling reads to reconstruct expressed transcripts, sophisticated algorithms can be then applied to estimate the expression levels of each transcript.
We review different methodologies to estimate the expression levels of microRNAs (miRNAs) using real-time quantitative PCR (qPCR).
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