PubMed: Methylome analysis using MeDIP-seq with low DNA concentrations.

Newsbot! · 03-10-2012, 02:11 AM

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Methylome analysis using MeDIP-seq with low DNA concentrations.

Nat Protoc. 2012;7(4):617-36

Authors: Taiwo O, Wilson GA, Morris T, Seisenberger S, Reik W, Pearce D, Beck S, Butcher LM

Abstract
DNA methylation is an epigenetic mark that has a crucial role in many biological processes. To understand the functional consequences of DNA methylation on phenotypic plasticity, a genome-wide analysis should be embraced. This in turn requires a technique that balances accuracy, genome coverage, resolution and cost, yet is low in DNA input in order to minimize the drain on precious samples. Methylated DNA immunoprecipitation-sequencing (MeDIP-seq) fulfils these criteria, combining MeDIP with massively parallel DNA sequencing. Here we report an improved protocol using 100-fold less genomic DNA than that commonly used. We show comparable results for specificity (>97%) and enrichment (>100-fold) over a wide range of DNA concentrations (5,000-50 ng) and demonstrate the utility of the protocol for the generation of methylomes from rare bone marrow cells using 160-300 ng of starting DNA. The protocol described here, i.e., DNA extraction to generation of MeDIP-seq library, can be completed within 3-5 d.

PMID: 22402632 [PubMed - in process]

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tanaybhatt · 04-25-2017, 04:06 AM

Can someone direct me to a published paper where DMR analysis has been done without taking the input in consideration (or without input subtraction/normalization)?

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03-10-2012, 02:11 AM	#1
Newsbot! RSS Posting Maniac Join Date: Feb 2008 Posts: 1,438	PubMed: Methylome analysis using MeDIP-seq with low DNA concentrations. Syndicated from PubMed RSS Feeds Methylome analysis using MeDIP-seq with low DNA concentrations. Nat Protoc. 2012;7(4):617-36 Authors: Taiwo O, Wilson GA, Morris T, Seisenberger S, Reik W, Pearce D, Beck S, Butcher LM Abstract DNA methylation is an epigenetic mark that has a crucial role in many biological processes. To understand the functional consequences of DNA methylation on phenotypic plasticity, a genome-wide analysis should be embraced. This in turn requires a technique that balances accuracy, genome coverage, resolution and cost, yet is low in DNA input in order to minimize the drain on precious samples. Methylated DNA immunoprecipitation-sequencing (MeDIP-seq) fulfils these criteria, combining MeDIP with massively parallel DNA sequencing. Here we report an improved protocol using 100-fold less genomic DNA than that commonly used. We show comparable results for specificity (>97%) and enrichment (>100-fold) over a wide range of DNA concentrations (5,000-50 ng) and demonstrate the utility of the protocol for the generation of methylomes from rare bone marrow cells using 160-300 ng of starting DNA. The protocol described here, i.e., DNA extraction to generation of MeDIP-seq library, can be completed within 3-5 d. PMID: 22402632 [PubMed - in process] More...

04-25-2017, 04:06 AM	#2
tanaybhatt Junior Member Location: Bangalore Join Date: Apr 2017 Posts: 3	DMR analysis without Input Can someone direct me to a published paper where DMR analysis has been done without taking the input in consideration (or without input subtraction/normalization)?