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A consequence would be that any promoter associated with the newly methylated CpG island would be monoallelically expressed, and the yield of transcript from that promoter would be half of the non-imprinted state.
The presence of ribosomal and transfer RNAs in our sequencing sample did result in a decreased yield of transcript information from coding RNAs (only ~10% of the sample at each time point was non-rRNA and non-tRNA transcripts); however, this protocol avoided the known biases introduced by current rRNA depletion methods [ 47].
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To estimate the yield of TCR transcripts that could be expected from typical RNA-seq experiments, we used Flux Simulator [ 19] to generate simulated RNA-seq data spiked with in silico recombined TCR transcripts, and processed these data as described in " Methods".
The coverage metrics completeness (width and read depth), and diagnostic yield (number of transcripts fully covered at 10x read depth) for dbCMMS and the exome are shown in [see Additional file 3].
Longer transcripts yield more skewing of transcript levels in the 3' end and a higher 3'/5' ratios of in vitro synthesized RNA.
The resultant nineteen hours of recordings were then transcribed, with repeated careful listening revealing ever more detail [ 9], to yield 564 pages of transcript.
Analysis of the microarray expression data yielded lists of transcripts that were differentially expressed (responded to PDGF-BB) with high statistical confidence in each of the four cell lines.
While proponents of these methods argue that the limitations are offset by improved yield, production of long transcript, reproducibility, and reduced amplification bias, we have found in practice that no single protocol is able to perform consistently in all four areas.
Since RNA isolation is different for the various species and results in different yields, quantitative comparison of transcript abundances was omitted.
However, their competition for the use of splicing machinery may reduce the yield of normal Ank1 transcript.
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.
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