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Series GSE77019 Query DataSets for GSE77019
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.
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:
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 (, 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.
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
Organization name Peking University
Street address Intergrated Science Building
City Beijing
ZIP/Postal code 100871
Country China
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Reanalysis of GSM1207815
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Reanalysis of GSM1240906
Reanalysis of GSM1240907
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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

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

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

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