Dear, All.
I did the bisulfate sequencing experiment to check the methylation percentage from the gDNA. I have 2 groups of mice and 3 mice each group. I have different number of clones from different mouse. While calculating I used Mouse number as 'n' to calculate the SEM. the methylation pattern showing different but the methylation percentage showing no different and have a huge bar.
I am thinking to use the individual clones as 'n' but I worry that that is not the best way to calculate my data.
did anyone ever do this kind of calculation?
please share me your opinion.
best,
Basta
Hi Basta
I think the usual approach here is to initially map predicted CpG islands using MethPrimer
https://www.urogene.org/methprimer/
You can then use that to plot positions of CpGs in your amplicon and create a grid for showing whether each island was or wasn’t methylated (eg black dots for not methylated and white dots for methylated). Example is in this paper here, Figure 6E
Article A Chimeric HS4-SAR Insulator (IS2) That Prevents Silencing a...
To answer your question about n numbers, in my opinion it’s better to use experimental replicates for the stats, rather than clones. But I have seen others just use clones for replicates - just be transparent when you report the data.
Thank you both John Counsell and Serafina Qin
.I willl learn your suggestion fist.
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