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Series GSE146129 Query DataSets for GSE146129
Status Public on Jun 22, 2020
Title IMPLICON: a high-resolution method to uncover DNA methylation at imprinted regions
Organisms Homo sapiens; Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Summary Genomic imprinting is an epigenetic phenomenon leading to parental allele specific expression. Dosage of imprinted genes is crucial for normal development and its dysregulation accounts for a number of human disorders. Imprinted expression is dictated by differences in DNA methylation between parental alleles at specific regulatory elements known as imprinting control regions (ICRs). Although a number of approaches can be used for methylation inspection at ICRs, we lack an easy and cost-effective method to simultaneously measure DNA methylation at multiple imprinted regions. Here, we present IMPLICON, a new high-throughput method measuring DNA methylation levels at imprinted regions with base-pair resolution and over 1000-fold genomic coverage. We initially designed this method to look at ICRs in adult tissues of inbred mice. Then, we validated in hybrid mice from reciprocal crosses for which we could discriminate methylation profiles in the two parental alleles. Lastly, we developed a human version of IMPLICON and detected imprinting errors in naïve human embryonic and induced pluripotent stem cells. We also provide rules and guidelines in which this method can be adapted to investigate the DNA methylation landscape of any set of genomic regions. In summary, IMPLICON is a rapid, cost-effective and scalable method, which could become the gold standard in both imprinting research and diagnostics.
Overall design [IMPLICON] Amplicon bisulfite libraries targetting imprinted control regions for mouse and human
Contributor(s) Klobučar T, Kreibich E, Krueger F, Arez M, Pólvora-Brandão D, von Meyenn F, Reik W, Teixeira da Rocha S, Eckersley-Maslin M
Citation(s) 32621604
Submission date Feb 28, 2020
Last update date Oct 02, 2020
Contact name Felix Krueger
Organization name Altos Labs
Department Bioinformatics
Street address Granta Park
City Cambridge
ZIP/Postal code CB21 6GP
Country United Kingdom
Platforms (2)
GPL15520 Illumina MiSeq (Homo sapiens)
GPL16417 Illumina MiSeq (Mus musculus)
Samples (30)
GSM4367011 15month_heart
GSM4367012 15month_liver
GSM4367013 15month_lung
BioProject PRJNA609357
SRA SRP251099

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Supplementary file Size Download File type/resource
GSE146129_RAW.tar 610.0 Kb (http)(custom) TAR (of COV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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