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During the initial analysis of the data we discovered widespread antisense regulation in agreement with previous tiling studies [9], [18], [19].
The percentage of transcribed DNA compared to total DNA is unknown with regards to the bacterial genomes considered in this paper, but is believed to be significantly higher than the percentage annotated today (based on previous tiling projects [37] [42]).
This range was selected because the lengths of most of 3′ extensions observed from previous tiling array analysis were less than 800 nt in length.
In this paper, we discussed a bioinformatics analysis on the novel RNA transcripts discovered in our previous tiling array work [ 4].
These data were normalized together with previous tiling array data generated for upf mutants (Kurihara et al. 2009) to reduce misidentification of unannotated transcripts, such as non-coding RNAs.
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Although these regions were found to be transcribed in previous ENCODE tiling array analysis of HL60, HeLa, and Gm06990 human cell lines (Figure S5, http://genome.ucsc.edu/ENCODE/pilot.html), there was no prior evidence that they represented 5' capped Pol II RNAs.
This discrepancy might reflect technical issues, as the previous study used tiling microarrays that provide less resolution and tend to have higher noise levels.
Previous whole-genome tiling arrays [ 25] that included the MHC were constructed from P1 artificial chromosomes (PACs) and bacterial artificial chromosomes (BACs), resulting in a resolution of approximately 100 Kb.
An analysis of Arabidopsis expression profiling data obtained from a previous study utilizing a tiling array [ 3] indicated that the expression of the TAS1/2/3 family was downregulated under drought and high-salinity stress).
However, of interest and consistent with the previous observation based on tiling arrays [ 20], RNA from adult Drosophila flies did not have as much non-exonic RNAs by mass as human cells, comprising approximately 11% of the polyA+ RNA and 19% of the RiboMinus RNA.
These previous studies have analyzed TIL numbers in different compartments ranging from primary tumour to PBMC, thus making comparison of results difficult.
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