GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE41273 Query DataSets for GSE41273
Status Public on Apr 15, 2013
Title Genome-wide analysis identifies aberrant methylation in Fragile X syndrome is specific to the FMR1 locus
Organism Homo sapiens
Experiment type Methylation profiling by genome tiling array
Summary Fragile X syndrome (FXS) is a common form of inherited intellectual disability and is caused by an expansion of CGG repeats located in the 5Õ untranslated region (UTR) of the FMR1 gene, leading to hypermethylation and silencing of this locus. While the dramatic increase in DNA methylation (DNAm) of the FMR1 full mutation allele is well documented, the extent that these changes affect DNAm throughout the entire gene and the rest of the genome remains unexplored. Here, we examine the genome-wide methylation in peripheral blood (N = 9) as well as induced pluripotent stem cells (iPSCs; N = 10) from FXS individuals and controls (N = 53 and 9, respectively) and find the expected significant DNAm differences in the FMR1 promoter and 5Õ UTR, but also that these changes inversely persist throughout the FMR1 gene body. Importantly, we find there are no additional differential methylated loci (DML) throughout the remainder of the genome, indicating that the aberrant methylation of the FMR1 in FXS is locus-specific and does not change DNAm genome-wide. This study provides a comprehensive methylation profile of FXS and refines mechanistic considerations of FMR1 silencing.
Overall design A total of 62 blood (53 controls + 9 Fragile X) samples analyzed using a linear regression model.
Contributor(s) Warren S, Chopra P
Citation(s) 23356558
Submission date Oct 02, 2012
Last update date Mar 22, 2019
Contact name Pankaj Chopra
Phone 404 727 0405
Organization name Emory University
Department Human Genetics
Lab Warren Lab
Street address 615 Michael St. NE, Ste. 375
City Atlanta
State/province GA
ZIP/Postal code 30322
Country USA
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (62)
GSM1013175 12582.s1
GSM1013176 11028.s1
GSM1013177 11046.s1
BioProject PRJNA176419

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
GSE41273_RAW.tar 183.1 Mb (http)(custom) TAR
GSE41273_blood_matrix_signal_intensities.txt.gz 255.9 Mb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap