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Comparison of sequencing coverage in relation to the GC content in 200-bp windows between T-WGBS and conventional WGBS. Supplementary Figure 8: Comparison of sequencing coverage in relation to the GC content in 200-bp windows between T-WGBS and conventional WGBS. Coverage versus local GC content in 200-bp windows, roughly the median length of genomic DNA in the library fragments, for WGBS (red) and T-WGBS (blue). Supplementary Figure 1: Control of size distribution of three DNA samples after tagmentation.
Supplementary Figure 2: PCR amplification curves and size distributions of T-WGBS libraries prepared from six different human blood samples. Supplementary Figure 4: Scatter plot versions of the comparative methylation levels shown in Figure 4a,b. For each sample, two lanes of T-WGBS data and three lanes of conventional WGBS were compared. Supplementary Figure 6: High consistency of methylation levels between T-WGBS and conventional WGBS. Supplementary Figure 7: Comparison of sequencing coverage of cytosines in CpG, CHG and CHH context (H can be A, C or T) between T-WGBS and conventional WGBS.
This entry was posted on April 16th, 2013 at 14:41 by Felix Kokocinski and is filed under Bioinformatics.

Did you know that you can plot different kinds of statistical graphs based upon your sequences in UGENE? You can see an example of how to plot the GC content graph for SARS coronavirus genome on attached screenshots. On attached screenshots you can see an example of how to download the NPTN gene sequence that became known due to the positive influence of its product Neuroplastin on the intelligence.
On attached screenshots you can see an example of how to tune and save the consensus sequence of a multiple alignment. Did you know how to find quickly occurrences of a sequence in a multiple alignment by means of UGENE?
We tried to make it as much easy as it takes from you to find a word on a web-browser page.
On the attached screenshot you can see an example of how to find the -10 element constituting promoters in prokaryotic cells. See more about sequence search in the UGENE Multiple Alignment Editor in our documentation. The base composition bias in the first bases of the T-WGBS reads is caused by the Tn5 transposase which has a slight base preference at certain positions of the integration target sequence (please see the paragraph entitled ‘Limitations’ in the INTRODUCTION for further information). The coverage appears stable in genomic regions with 100–400 cytosines, likely because the majority of 1-kb regions has a cytosine density between 10% and 40%.

The human genome is a mosaic of GC-rich and GC-poor regions, of around 300kb in length, called isochores.
In the appeared dialog you can make up complex queries including the information about the scientist discovered the sequence, the name of a corresponding gene or organism.
Variation becomes larger in the two extremes of the cytosine density for both T-WGBS and conventional WGBS due to low counts in each category.
This GC effect is unimodal: both GC-rich fragments and AT-rich fragments are underrepresented in the sequencing results.
After that UGENE provides the list of sequences satisfying specified criteria, and you can choose which of them are to be saved on your computer. Here you can specify where the file with the consensus sequence is to be saved to and in which format. Consistency defined as less than 0.2 (20%) difference in methylation level in windows of 5 CpGs. This is especially true for next-generation sequencing where the DNA being sequenced has gone through multiple rounds of PCR amplification.

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