Ns126:GMPOR: Difference between revisions
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2016-9-7: Download 4 differentiation SRR files(SRR2011294/SRR2011297/SRR2011296/SRR2011295) | 2016-9-7: Download 4 differentiation SRR files(SRR2011294/SRR2011297/SRR2011296/SRR2011295) | ||
*remove all single-cell methylome | *remove all single-cell methylome | ||
*remove SRX1126148 | *remove SRX1126148,SRX1091395,SRX1091396 since mapping ratio<5% | ||
*37 + 4 samples | |||
cd /home/shg047/oasis/mouse/fastq | cd /home/shg047/oasis/mouse/fastq |
Revision as of 08:52, 9 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
- 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
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
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 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.