Ns126:Calendar/NOTES/2015-6-12: Difference between revisions

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>Shicheng
>Shicheng
 
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==Method==
==Method==
*Download human and mice reprogramming dataset
*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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==Result==
==Result==
=== Dendrogram and PCA analysis===
*GSE57179: human, 4 hiPS, 4 SCNT, 2 ES and 1 fibroblasts
**Description: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE57179
**Download: ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE57nnn/GSE57179/suppl/
*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 mice can be found here
=== Differential Methylation Site Analysis===
* human
**number of DMS


*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


* mice
**number of DMS


==Conclusion==
==Conclusion==
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*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.


*
*For mice ips and SCNT data, the methylation status of 4909250 CpG were shared by 9 samples(1 ES, 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==
==Highlight==
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*PCA analysis loading can be found here:  [[File:Figure2.PCA.loading.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]]
*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
*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.

Latest revision as of 01:52, 13 June 2015

Genome-wide DNA methylation profile of reprogramming[edit]

Method[edit]

  • 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[edit]

Dendrogram and PCA analysis[edit]

  • 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

Differential Methylation Site Analysis[edit]

  • human
    • number of DMS


  • mice
    • number of DMS

Conclusion[edit]

  • 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 mice ips and SCNT data, the methylation status of 4909250 CpG were shared by 9 samples(1 ES, 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[edit]

Supplemenatry[edit]

  • For mice

Reference[edit]

  • 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.