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Series GSE19937 Query DataSets for GSE19937
Status Public on Apr 12, 2010
Title Human embryonic stem cells HELP-tagging cytosine methylation data (Albert Einstein College of Medicine)
Organism Homo sapiens
Experiment type Methylation profiling by high throughput sequencing
Summary Background: To perform epigenome-wide association studies in human disease, assays need to be comprehensive and quantitative while remaining cost-effective. We explored how the strengths of prior tag-based cytosine methylation assays based on massively-parallel sequencing can be maximised analytically. Results: We find that the use of the EcoP15I restriction enzyme to generate long tags and the normalisation of methylation-sensitive by methylation-insensitive restriction enzyme representations greatly improve assay performance. When exploring sources of bias, we find that the length of the restriction fragment has moderate effects on EcoP15I digestion, while base composition exerts minimal effects. We detail the analytical workflow that maximises the quantitative capabilities of this modified assay. Also revealed are polymorphic sequences in the genome that could confound microarray, bisulphite sequencing or mass spectrometry-based assays, and a position effect causing hypomethylation of transposable elements near gene promoters. Conclusions: The new combined assay, referred to as HELP-tagging, interrogates over 1.8 million loci in the human genome quantitatively with a single lane of Illumina sequencing. When the goal is to study not only CG-dense sequence but also the CG-depleted majority of the genome, this assay system should be suitable.
 
Overall design Three MspI reference, one HpaII test
 
Contributor(s) Greally JM, Suzuki M
Citation(s) 20359321
Submission date Jan 19, 2010
Last update date May 15, 2019
Contact name John Greally
E-mail(s) john.greally@einsteinmed.edu
Phone 7186781234
Organization name Albert Einstein College of Medicine
Department Genetics
Street address 1301 Morris Park Avenue
City Bronx
State/province NY
ZIP/Postal code 10461
Country USA
 
Platforms (1)
GPL9115 Illumina Genome Analyzer II (Homo sapiens)
Samples (4)
GSM498218 Human ES MspI rep1
GSM498219 Human ES MspI rep2
GSM498220 Human ES MspI rep3
Relations
SRA SRP002221
BioProject PRJNA122627

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
GSE19937_RAW.tar 228.3 Mb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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