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Series GSE52588 Query DataSets for GSE52588
Status Public on Mar 03, 2015
Title Identification of a DNA methylation signature in blood from subjects affected by Down syndrome
Organism Homo sapiens
Experiment type Methylation profiling by array
Summary Down syndrome is characterized by a wide spectrum of clinical signs, which include cognitive and endocrine disorders and haematological abnormalities. Although it is well established that the causative defect of Down syndrome is the trisomy of chromosome 21, the molecular bases of Down syndrome phenotype are still largely unknown. We used the Infinium HumanMethylation450 BeadChip to investigate DNA methylation patterns in whole blood from 29 subjects affected by Down syndrome (DS), using their healthy relatives as controls (mothers and unaffected siblings). This family-based model allowed us to monitor possible confounding effects on DNA methylation patterns deriving from genetic and environmental (lifestyle) factors. The identified epigenetic signature of Down syndrome includes differentially methylated regions that, although enriched on chromosome 21, interest most of the other chromosomes and can be functionally linked to the developmental and haematological defects characteristic of the disease.
Overall design DNA was extracted from whole peripheral blood using the QIAamp 96 DNA Blood Kit (QIAGEN) and quantified by Quant-iT™ PicoGreen (Invitrogen). Sodium bisulphite conversion of 500 ng of each sample was performed using the EZDNA Methylation-Gold Kit according to the manufacturer's recommendation for Illumina Infinium Assay. 4 ul of bisulfite converted DNA were hybridized on Infinium HumanMethylation 450 BeadChip, following manufacturer’s instructions. Arrays were scanned by HiScan SQ scanner (Illumina) and the intensities of the images were extracted using GenomeStudio (2010.3) Methylation module (1.8.5) software. Methylation levels of each CpG is reported as beta value.
Contributor(s) Bacalini MG, Gentilini D, Boattini A, Giampieri E, Pirazzini C, Giuliani C, Fontanesi E, Scurti M, Remondini D, Capri M, Cocchi G, Ghezzo A, Del Rio A, Luiselli D, Vitale G, Mari D, Castellani G, Fraga M, Di Blasio AM, Salvioli S, Franceschi C, Garagnani P
Citation(s) 25701644, 25678027, 25701668
Submission date Nov 20, 2013
Last update date Aug 14, 2019
Contact name Maria Giulia Bacalini
Phone 00390512094748
Organization name IRCCS Istituto delle Scienze Neurologiche di Bologna
Department Brain Aging Laboratory
Street address Via Altura 3
City Bologna
ZIP/Postal code 40139
Country Italy
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (87)
GSM1272122 genomic DNA from peripheral blood, subject affected by Down syndrome, 1001
GSM1272123 genomic DNA from peripheral blood, subject affected by Down syndrome, 1003
GSM1272124 genomic DNA from peripheral blood, subject affected by Down syndrome, 1007
BioProject PRJNA230264

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
GSE52588_RAW.tar 183.1 Mb (http)(custom) TAR
GSE52588_raw_data.txt.gz 194.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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