Ns126:Calendar/NOTES/2015-6-12: Difference between revisions
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=Genome-wide DNA methylation profile of reprogramming= | =Genome-wide DNA methylation profile of reprogramming= | ||
== | ==Method== | ||
*Merge genome-wide DNA methylation data of human and mice | *Merge genome-wide DNA methylation data of human and mice | ||
*Dendrogram based on genome-wide DNA methylation data(Figure 1a and 1b) | *Dendrogram based on genome-wide DNA methylation data(Figure 1a and 1b) | ||
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*heatmap based on DMR and DMRs in CpG Shore region (Figuare 1c,1d,1e and 1f) | *heatmap based on DMR and DMRs in CpG Shore region (Figuare 1c,1d,1e and 1f) | ||
== | ==Result== | ||
*Dendrogram based on genome-wide DNA methylation for human can be found here [[File:Figure1.dendrogram.euclidean.ward.hclust.pdf]] | *Dendrogram based on genome-wide DNA methylation for human can be found here [[File:Figure1.dendrogram.euclidean.ward.hclust.pdf]] | ||
*Dendrogram based on genome-wide DNA methylation for mice can be found here | *Dendrogram based on genome-wide DNA methylation for mice can be found here | ||
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== | ==Conclusion== | ||
*For human ips and SCNT data, the methylation status of 4377908 CpG were shared by 11 samples(2 ES, 1 Fibroblast, 4 ips and 4 SCNT). PCA analysis based on the genome-wide DNA methylation data showed the first and second principle component can explain almost 50% variances. In the dimension of first component fibroblast were obviously separated with ES,ips and SCNT. In the dimension of the second component, ES was separated with ips and SCNT with clear boundary. | *For human ips and SCNT data, the methylation status of 4377908 CpG were shared by 11 samples(2 ES, 1 Fibroblast, 4 ips and 4 SCNT). PCA analysis based on the genome-wide DNA methylation data showed the first and second principle component can explain almost 50% variances. In the dimension of first component fibroblast were obviously separated with ES,ips and SCNT. In the dimension of the second component, ES was separated with ips and SCNT with clear boundary. | ||
== | ==Highlight== |
Revision as of 21:55, 12 June 2015
Genome-wide DNA methylation profile of reprogramming
Method
- Merge genome-wide DNA methylation data of human and mice
- Dendrogram based on genome-wide DNA methylation data(Figure 1a and 1b)
- PCA analysis based on genome-wide DNA methylation data(Figure 2a and 2b)
- heatmap based on DMR and DMRs in CpG Shore region (Figuare 1c,1d,1e and 1f)
Result
- Dendrogram based on genome-wide DNA methylation for human can be found here File:Figure1.dendrogram.euclidean.ward.hclust.pdf
- Dendrogram based on genome-wide DNA methylation for mice can be found here
- PCA analysis based on genome-wide DNA methylation for human can be found here
- PCA analysis based on genome-wide DNA methylation for mice can be found here
Conclusion
- For human ips and SCNT data, the methylation status of 4377908 CpG were shared by 11 samples(2 ES, 1 Fibroblast, 4 ips and 4 SCNT). PCA analysis based on the genome-wide DNA methylation data showed the first and second principle component can explain almost 50% variances. In the dimension of first component fibroblast were obviously separated with ES,ips and SCNT. In the dimension of the second component, ES was separated with ips and SCNT with clear boundary.