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Series GSE60225 Query DataSets for GSE60225
Status Public on Dec 12, 2014
Title Application of a low cost array-based technique - TAB-Array - for quantifying and mapping both 5mC and 5hmC at single base resolution.
Organism Homo sapiens
Experiment type Methylation profiling by genome tiling array
Summary 5-hydroxymethylcytosine (5hmC), an oxidized derivative of 5-methylcytosine (5mC), has been implicated as an important epigenetic regulator of mammalian development. Current procedures use cost-prohibitive DNA sequencing methods to discriminate 5hmC from 5mC, limiting their accessibility to the scientific community. Here we report a method that combines TET-assisted bisulfite conversion with Illumina 450K DNA methylation arrays for a low-cost high-throughput approach that distinguishes 5hmC and 5mC signals. Implementing this approach, termed TAB-array, we assessed DNA methylation dynamics in the differentiation of human pluripotent stem cells into cardiovascular and neural progenitors. With the ability to discriminate 5mC and 5hmC, we found a much larger number of dynamically methylated genomic regions implicated in the development of these lineages than we could detect by 5mC analysis alone. The increased resolution and accuracy afforded by this approach provides a powerful means to investigate the distinct contributions of 5mC and 5hmC in human development and disease.
Overall design We generated illumina 450k DNA methylation data for a total of 9 sample groups with two biological replicates for each group. Data for 4/9 groups were generated from glucosylated and bisulfite converted DNA, from human induced plurupotent stem cells (hIPSCs), differentiated cardiovascular progenitors (CVPs), differentiated neural progenitors (NPCs), and fibroblasts. Data for the next 4/9 groups were generated from glucosylated, TET-oxidized and bisulfite converted DNA, from and included replicates of hIPSCs, CVPs, NPCs, and fibroblasts. Data for the last group was generated from standard bisulfite converted DNA (not glucosylated) from fibroblasts.
Contributor(s) Nazor KL, Peterson SE, Boland MJ, Bibikova M, Klotzle B, Yu M, Glenn-Pratola VL, Schell JP, Coleman RL, Cabral-da-Silva MC, Schmidt U, He C, Loring JF, Fan J
Citation(s) 25179373
Submission date Aug 08, 2014
Last update date Mar 22, 2019
Contact name Kristopher L. Nazor
Organization name The Scripps Research Institute
Department Regenerative Medicine
Lab Loring
Street address 10550 North Torrey Pines Road
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (18)
GSM1468312 HiPSC68_undiff_5mC_rep1
GSM1468313 HiPSC68_undiff_5mC_rep2
GSM1468314 CARDIAC_5mC_rep1
BioProject PRJNA257792

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
GSE60225_RAW.tar 183.1 Mb (http)(custom) TAR
GSE60225_methylated_unmethylated.txt.gz 42.8 Mb (ftp)(http) TXT
Processed data included within Sample table

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