|
| Status |
Public on Sep 01, 2016 |
| Title |
The non-CG methylation is cell-type specific and conserved between human and mouse [Third-party reanalysis] |
| Sample organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Methylation profiling by high throughput sequencing
Third-party reanalysis
|
| Summary |
The non-CG methylations are abundant in several mammalian cell types, while their biological functions are largely unknown. We gathered 51 DNA methylomes in both human and mouse, covering brain neuron cells, embryonic stem (ES) and induced pluripotent stem (iPS) cells, primordial germ cells (PGC) and oocytes. Then a two-dimensional comparison on non-CG methylation was carried out across cell types and species. We employed an unbiased sub-motif prediction method and identified CW (W can be A or T) as the representative non-CG methylation context. We further showed mCW was significantly distinct from CC methylation (mCC) in both context and genomic distribution. Our studies on sequence preferences and genomic region enrichment revealed that mCW was cell-type specific and conserved between human and mouse. We reported young long interspersed nuclear elements-1 (LINE-1) elements tended to be deprived of mCW in brain for both species. Interestingly, both human Alu elements and mouse B1 elements were found to prefer high mCW at specific loci during evolution. Additionally, we reported a peak of CG methylation (mCG) at the promoter of young LINE-1 element in PGC, in contrast to the global CG demethylation. Lastly, we confirmed strand-skewed non-CG methylation in mouse ES intronic region, and showed the strand-specific distributions of mCW in LINE elements are also cell-type specific and conserved. Our findings indicate that mCW is conserved in species, dynamically regulated during development, and likely to guide the evolution of transposon elements.
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| Overall design |
In this study, 41 samples were re-aligned from raw sequencing data using BS-Seeker2.
The raw data available from the samples associated with the following Series:
GSE11034
GSE30199
GSE30206
GSE34864
GSE37202
GSE42923
GSE46644
GSE46710
GSE49828
GSE51239
GSE52331
GSE56650
GSE61330
GSE61457
GSE63394
GSE63818
The accession numbers of the re-analyzed GEO Samples (GSMnnnnn; associated with each processed data file) are indicated in the 'complete_metadata.xls'.
Please note that several raw data files are downloaded directly from SRA, DDBJ (https://trace.ddbj.nig.ac.jp), European Nucleotide Archive, and the public accession numbers for the raw data associated with each processed data file are indicated in the 'complete_metadata.xls' as well.
The 'DATA PROCESSING PIPELINE' section (in the 'complete_metadata.xls') describes the re-analysis details.
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| Contributor(s) |
Guo W, Zhang M, Wu H |
| Citation(s) |
27573482 |
| Submission date |
Jan 20, 2016 |
| Last update date |
Sep 01, 2016 |
| Contact name |
Weilong Guo |
| E-mail(s) |
guoweilong@126.com
|
| Organization name |
Peking University
|
| Street address |
Intergrated Science Building
|
| City |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
| |
|
| Relations |
| Reanalysis of |
GSM1053456 |
| Reanalysis of |
GSM1135081 |
| Reanalysis of |
GSM1135082 |
| Reanalysis of |
GSM1204459 |
| Reanalysis of |
GSM1204460 |
| Reanalysis of |
GSM1207815 |
| Reanalysis of |
GSM1207816 |
| Reanalysis of |
GSM1240905 |
| Reanalysis of |
GSM1240906 |
| Reanalysis of |
GSM1240907 |
| Reanalysis of |
GSM1263221 |
| Reanalysis of |
GSM1263222 |
| Reanalysis of |
GSM1366370 |
| Reanalysis of |
GSM1366371 |
| Reanalysis of |
GSM1502486 |
| Reanalysis of |
GSM1502487 |
| Reanalysis of |
GSM1505240 |
| Reanalysis of |
GSM1548017 |
| Reanalysis of |
GSM1548019 |
| Reanalysis of |
GSM1677818 |
| Reanalysis of |
GSM1677819 |
| Reanalysis of |
GSM1677830 |
| Reanalysis of |
GSM1677832 |
| Reanalysis of |
GSM1677833 |
| Reanalysis of |
GSM1677835 |
| Reanalysis of |
GSM1677836 |
| Reanalysis of |
GSM278895 |
| Reanalysis of |
GSM748786 |
| Reanalysis of |
GSM748787 |
| Reanalysis of |
GSM753569 |
| Reanalysis of |
GSM830248 |
| Reanalysis of |
GSM830249 |
| Reanalysis of |
GSM856556 |
| Reanalysis of |
GSM856557 |
| Reanalysis of |
GSM913595 |
| Reanalysis of |
GSM913596 |
| BioProject |
PRJNA309298 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE77019_complete_metadata.xls.gz |
20.5 Kb |
(ftp)(http) |
XLS |
| GSE77019_hBrain_AdFront_Wen.CGmap.gz |
4.7 Gb |
(ftp)(http) |
CGMAP |
| GSE77019_hBrain_FCN_Zill.CGmap.gz |
5.6 Gb |
(ftp)(http) |
CGMAP |
| GSE77019_hBrain_Hs1570_Zeng.CGmap.gz |
4.1 Gb |
(ftp)(http) |
CGMAP |
| GSE77019_hBrain_Hs1832_Zeng.CGmap.gz |
2.5 Gb |
(ftp)(http) |
CGMAP |
| GSE77019_hES_PBAT_Tang.CGmap.gz |
3.3 Gb |
(ftp)(http) |
CGMAP |
| GSE77019_hFPGC_10wE1_GuoF.CGmap.gz |
3.1 Gb |
(ftp)(http) |
CGMAP |
| GSE77019_hFPGC_11wE1_GuoF.CGmap.gz |
2.9 Gb |
(ftp)(http) |
CGMAP |
| GSE77019_hFPGC_17wE1_GuoF.CGmap.gz |
1.9 Gb |
(ftp)(http) |
CGMAP |
| GSE77019_hFPGC_7w_Tang.CGmap.gz |
4.0 Gb |
(ftp)(http) |
CGMAP |
| GSE77019_hFPGC_UW160_Gkoun.CGmap.gz |
1.6 Gb |
(ftp)(http) |
CGMAP |
| GSE77019_hMPGC_10wE2_GuoF.CGmap.gz |
2.3 Gb |
(ftp)(http) |
CGMAP |
| GSE77019_hMPGC_19wE1_GuoF.CGmap.gz |
2.3 Gb |
(ftp)(http) |
CGMAP |
| GSE77019_hMPGC_19wE2_GuoF.CGmap.gz |
2.6 Gb |
(ftp)(http) |
CGMAP |
| GSE77019_hMPGC_9w_Tang.CGmap.gz |
3.3 Gb |
(ftp)(http) |
CGMAP |
| GSE77019_hMPGC_UW165_Gkoun.CGmap.gz |
380.9 Mb |
(ftp)(http) |
CGMAP |
| GSE77019_hOocyte_AmpMinus_Okae.CGmap.gz |
1.8 Gb |
(ftp)(http) |
CGMAP |
| GSE77019_hOocyte_AmpPlus_Okae.CGmap.gz |
2.0 Gb |
(ftp)(http) |
CGMAP |
| GSE77019_hOocyte_Rrbs_GuoHS.CGmap.gz |
70.7 Mb |
(ftp)(http) |
CGMAP |
| GSE77019_mBrain_129_Xie.CGmap.gz |
3.2 Gb |
(ftp)(http) |
CGMAP |
| GSE77019_mBrain_Cast_Xie.CGmap.gz |
2.4 Gb |
(ftp)(http) |
CGMAP |
| GSE77019_mBrain_F1i_Xie.CGmap.gz |
3.9 Gb |
(ftp)(http) |
CGMAP |
| GSE77019_mBrain_Rrbs_Meis.CGmap.gz |
17.0 Mb |
(ftp)(http) |
CGMAP |
| GSE77019_mBrain_Rrbs_Smith.CGmap.gz |
32.5 Mb |
(ftp)(http) |
CGMAP |
| GSE77019_mBrain_Wt_GuoJU.CGmap.gz |
4.5 Gb |
(ftp)(http) |
CGMAP |
| GSE77019_mES_2line_Kob.CGmap.gz |
2.4 Gb |
(ftp)(http) |
CGMAP |
| GSE77019_mES_J1_Seis.CGmap.gz |
3.1 Gb |
(ftp)(http) |
CGMAP |
| GSE77019_mES_P0_Ficz.CGmap.gz |
1.4 Gb |
(ftp)(http) |
CGMAP |
| GSE77019_mES_Wt_Li.CGmap.gz |
3.4 Gb |
(ftp)(http) |
CGMAP |
| GSE77019_mES_Wt_Stad.CGmap.gz |
3.7 Gb |
(ftp)(http) |
CGMAP |
| GSE77019_mES_p01Rrbs_Smith.CGmap.gz |
30.6 Mb |
(ftp)(http) |
CGMAP |
| GSE77019_mES_p02Rrbs_Smith.CGmap.gz |
34.7 Mb |
(ftp)(http) |
CGMAP |
| GSE77019_mES_p032Rrbs_Smith.CGmap.gz |
29.8 Mb |
(ftp)(http) |
CGMAP |
| GSE77019_mFPGC_E13p5_Seis.CGmap.gz |
1.1 Gb |
(ftp)(http) |
CGMAP |
| GSE77019_mFPGC_E16p5_Seis.CGmap.gz |
1.4 Gb |
(ftp)(http) |
CGMAP |
| GSE77019_mMPGC_E13p5_Seis.CGmap.gz |
2.5 Gb |
(ftp)(http) |
CGMAP |
| GSE77019_mMPGC_E16p5_Kob.CGmap.gz |
3.5 Gb |
(ftp)(http) |
CGMAP |
| GSE77019_mMPGC_E16p5_Seis.CGmap.gz |
3.1 Gb |
(ftp)(http) |
CGMAP |
| GSE77019_mOocyte_GV_Kob.CGmap.gz |
1.0 Gb |
(ftp)(http) |
CGMAP |
| GSE77019_mOocyte_GV_Shira.CGmap.gz |
3.5 Gb |
(ftp)(http) |
CGMAP |
| GSE77019_mOocyte_Rrbs_GuoF.CGmap.gz |
33.1 Mb |
(ftp)(http) |
CGMAP |
| GSE77019_mOocyte_Rrbs_Shen.CGmap.gz |
35.8 Mb |
(ftp)(http) |
CGMAP |
| Processed data are available on Series record |
