Ns126:Calendar/NOTES/2015-6-12: Difference between revisions
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*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 | ||
*PCA analysis based on genome-wide DNA methylation for human can be found here [[File:Figure2.PC13.pdf]] | |||
*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 | *PCA analysis based on genome-wide DNA methylation for mice can be found here | ||
Revision as of 22:46, 12 June 2015
Genome-wide DNA methylation profile of reprogramming
Method
- Download human and mice reprogramming dataset
- 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
- GSE57179: human, 4 hiPS, 4 SCNT, 2 ES and 1 fibroblasts
- 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 File:Figure2.PC13.pdf
- 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.
Highlight
Supplemenatry
- For human
- PCA analysis PC2 and PC3 can be found here: File:Figure2.PC23.pdf
- PCA analysis PC1 and PC3 can be found here:File:Figure2.PC13.pdf
- PCA analysis loading can be found here: File:Figure2.PCA.loading.pdf
- PCA analysis variance can be found here: File:Figure2.PCA.loading.total.increasing.pdf
- correlation matrix between different samples: File:Table1.correlation.matrix.txt
- For mice
Reference
- 1.Ma H, Morey R, O'Neil RC, He Y, Daughtry B, Schultz MD, et al. Abnormalities in human pluripotent cells due to reprogramming mechanisms. Nature. 2014;511(7508):177-83. Epub 2014/07/11.
- 2.
- 3.