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Series GSE63527 Query DataSets for GSE63527
Status Public on Aug 24, 2017
Title Tissue-specific DNA methylation is conserved across species and driven by primary sequence conservation
Organisms Mus musculus; Rattus norvegicus
Experiment type Methylation profiling by high throughput sequencing
Summary Tissue specific differentially methylated regions (DMRs) have been shown to play important roles in tissue specification, but little is known about the conservation pattern of genome-wide DNA methylation distribution that encodes tissue specifity. Using a comparative approach, we identified and compared the tissue-specific DNA methylation patterns of the rat against that of mouse and human across three common tissue types. We found that 10%-40% of this tissue-specific DNA methylation pattern is conserved, and this epigenetic onservation is associated with the conservation of tissue specific TFBS.
 
Overall design To evaluate the epigenetic evolution of tissue specific DMRs, we generated complete DNA methylome maps for rat blood, brain, sperm, and mouse blood by integrating data from methylated DNA immunoprecipitation sequencing (MeDIP-seq) and methylation-sensitive restriction enzyme sequencing (MRE-seq). We have also profiled DNA methylation datasets for mouse brain, sperm, and human blood, brain, sperm, as well as ChIP-seq data in the matching tissue types. These data were collected from the Human Epigenome Roadmap and MouseENCODE consortia;
Mouse Brain: GSE53694 [GSM1299110, GSM1299111]
Mouse Sperm: GSE49623 [GSM1202750-GSM1202753]
Human Blood: GSE16368 [GSM543023]
Human Brain: SRP002318
Human Sperm: GSE30340 [GSM752295, GSM752296]
 
Contributor(s) Zhou J, Wang T, Cicero TJ, Li D, Xing X
Citation(s) 28899353
Submission date Nov 21, 2014
Last update date Jul 31, 2019
Contact name Daofeng Li
E-mail(s) lidaof@gmail.com
Phone (314) 286-0866
Organization name Washington University in St. Louis
Department Genetics
Lab Ting Wang Lab
Street address 4515 McKinley Avenue
City SAINT LOUIS
State/province MO
ZIP/Postal code 63110
Country USA
 
Platforms (2)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL14844 Illumina HiSeq 2000 (Rattus norvegicus)
Samples (8)
GSM1551778 Rat Blood MeDIP-seq
GSM1551779 Rat Brain MeDIP-seq
GSM1551780 Rat Sperm MeDIP-seq
Relations
BioProject PRJNA268149
SRA SRP050115

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
GSE63527_RAW.tar 1.7 Gb (http)(custom) TAR (of BIGWIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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