Ns126:GMPOR: Difference between revisions

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>Shicheng
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Line 60: Line 60:
  cd /home/shg047/oasis/mouse/mergeHapinfo/mf
  cd /home/shg047/oasis/mouse/mergeHapinfo/mf
  perl /home/shg047/bin/hapinfo2mf.pl /home/shg047/oasis/mouse/mergeHapinfo/mf > output.mf
  perl /home/shg047/bin/hapinfo2mf.pl /home/shg047/oasis/mouse/mergeHapinfo/mf > output.mf
  [[File:4FD2.tm.png|200px]]
  [[File:4FD2.tm.png|400px]]


* hapinfo2mf (5me)
* hapinfo2mf (5me)

Revision as of 20:40, 10 September 2016

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)


wget ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1027nnn/GSM1027571/suppl/GSM1027571_DNA_CpG_coverage_E14_serum_LIF.bedGraph.gz &
wget ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1027nnn/GSM1027571/suppl/GSM1027571_DNA_CpG_methcounts_E14_serum_LIF.bedGraph.gz &
wget ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1027nnn/GSM1027572/suppl/GSM1027572_DNA_CpG_coverage_E14_2i_adapted.bedGraph.gz & 
wget ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1027nnn/GSM1027572/suppl/GSM1027572_DNA_CpG_methcounts_E14_2i_adapted.bedGraph.gz &
wget ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1127nnn/GSM1127953/suppl/GSM1127953_DNA_CpG_E14_serum_rep.bedGraph.gz &
wget ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1127nnn/GSM1127954/suppl/GSM1127954_DNA_CpG_E14_2i_adapted_rep.bedGraph.gz &

Result

Dendrogram and PCA analysis

  • 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

Distance between ES, IPS and HF

The distance between HF and ES as well as IPS is very large while actually IPS and ES are very similar, enclose figure showed ES, HF and two kinds of IPS (with two different inducing factor/method) in PC1-PC2 space.File:Ips ES HF.pdf.pdf, please check the code: File:PCAanalysis4GSE54115.R.txt

Mouse MHB

2016-9-7: Download 4 differentiation SRR files(SRR2011294/SRR2011297/SRR2011296/SRR2011295)

  • remove all single-cell methylome
  • remove SRX1126148,SRX1091395,SRX1091396 since mapping ratio<5%
  • 37 + 4 samples
cd /home/shg047/oasis/mouse/fastq
perl ~/bin/trimGolrePBS.pl FastqMatchConfig.txt nonsubmit
qsub SRR2011294_1.fastq.gz.job
qsub SRR2011295_1.fastq.gz.job
qsub SRR2011296_1.fastq.gz.job
qsub SRR2011297_1.fastq.gz.job
perl ~/bin/bismark2bamPBS.pl FastqMatchConfig.txt nosubmit
qsub SRR2011294_1.fastq.gz.job
qsub SRR2011295_1.fastq.gz.job
qsub SRR2011296_1.fastq.gz.job
qsub SRR2011297_1.fastq.gz.job
cd /home/shg047/oasis/mouse/mergeHapinfo
perl ~/bin/hapinfo2LDR2ByBed.pl /home/shg047/oasis/mouse/RD/hapinfo/Mouse.MHB.Alice.RD90_80up_R0.5.bed Adult.hapinfo.txt > Adult.R2.txt
cd /home/shg047/oasis/mouse/mergeHapinfo
perl ~/bin/hapinfo2LDR2ByBed.pl /home/shg047/oasis/mouse/RD/hapinfo/Mouse.MHB.Alice.RD90_80up_R0.5.bed mESC.hapinfo.txt > mESC.R2.txt
cd /home/shg047/oasis/mouse/mergeHapinfo/mf
perl /home/shg047/bin/hapinfo2mf.pl /home/shg047/oasis/mouse/mergeHapinfo/mf > output.mf
File:4FD2.tm.png
  • hapinfo2mf (5me)
cd /home/shg047/oasis/mouse/mergeHapinfo/mf
perl ~/bin/hapinfo2mf.pl
grep chr10:100004267-100004288 output.mf
File:DD51.tm.png

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 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

Supplemenatry

  • 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.