This group is a platform to discuss and share information about epigenetics and related methods.

• Azeem Mehmood Butt

  Transcription control elements

  Is it possible to predict transcriptonal control elements in humans? Can you recommend any software or tools to do this?

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• Oliver Bischof

  Analysis of LincRNA expression from RNA Seq

  I am looking for an easy way to determine the expression pattern of lincRNAs from RNASeq data. Could anyone direct me to potentially user friendly software?

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  • 
    Oliver Bischof replied

    Thanx alot for your input, Michal.

    23 days ago
• Renaud Massart

  Software for next generation sequencing data, microarray data.

  Could anyone recommend "friendly" softwares or software suites (genomatix... ?) to analyze and integrate whole genome sequencing and/or microarrays data?

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  • 
    Miguel R Branco replied

    I recommend SeqMonk for sequencing data (RNA, ChIP, bisulphite, HiC, ...). It is dead easy to use, works as a data browser and there is an ever-growing number of quantification and other analysisI recommend SeqMonk for sequencing data (RNA, ChIP, bisulphite, HiC, ...). It is dead easy to use, works as a data browser and there is an ever-growing number of quantification and other analysis tools in there with which you can do a lot. There might be downstream or other analyses that you're interested in for which a bit of programming goes a long way, but SeqMonk does plenty. It's predecessor, ChipMonk, deals with microarray data but it hasn't been as actively updated as SeqMonk.

    24 days ago
• Mozart Marins

  Has anyone used the myseq illumina plataform forchip-seq?

  Epigenetics

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  • 
    Matthias Schaefer replied

    Hi Ix Zhao, agree with what? Don't waste our time with agreeing.

    Apr 11, 2012
• Chen Xiang-song

  aza treatment for loss of DNA methylation

  We know that 5-aza-2'deoxycitydine treatment can cause loss of DNA methylation, however I have been confused with the mechanisms. Will the DNA methylation be recoverd after several generationsWe know that 5-aza-2'deoxycitydine treatment can cause loss of DNA methylation, however I have been confused with the mechanisms. Will the DNA methylation be recoverd after several generations without aza?

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    Matthias Schaefer replied

    Hi Chen Xiang-song, What about Pubmed or the library at your university? 5-aza has been used for quite a while and you will find lots of papers describing the mechanism, targets and the basics ofHi Chen Xiang-song, What about Pubmed or the library at your university? 5-aza has been used for quite a while and you will find lots of papers describing the mechanism, targets and the basics of cytosine methylation there. Why are you even asking such basic questions when you got a computer in front of you including search engines and a keyboard?

    Mar 24, 2012
• Brian Dias

  No amplification in qPCR using Input DNA as template

  I’ve done a ChIP twice now (independent samples), and while I get amplification for genes using my immunoprecipitated samples as template, I get no amplification using Input DNA as my template. AnyI’ve done a ChIP twice now (independent samples), and while I get amplification for genes using my immunoprecipitated samples as template, I get no amplification using Input DNA as my template. Any ideas? I just repeated the qPCR and got amplification in 2 out of 6 input DNA template rxns (without having done anything different than my previous qPCR). The no amplification and now 2/6 being amplified is baffling.

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    Brian Dias replied

    Hi Elizabeth, Francesco, Kathrin, Thanks for the info. I will incorporate your suggestions into my experimental design. Hi Beatriz, I treat the Input DNA the same way i treat theHi Elizabeth, Francesco, Kathrin, Thanks for the info. I will incorporate your suggestions into my experimental design. Hi Beatriz, I treat the Input DNA the same way i treat the immunoprecipitated samples. I take out the Input DNA and store at -20C as an aliquot before i put in the antibodies, then i take out the Input DNA after the last wash of the immunoprecipitated samples, make up the volume to 200ul using my Elution soluton (NaHCO3, SDS, TE), and then PCI extraction as with my eluted immunoprecipitated samples. No reverse cross-linking required because i do an N-ChIP protocol. -Brian

    Mar 15, 2012

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  • 
    John Holloway replied

    My students always enjoy this one: http://www.youtube.com/watch?v=RQbNuuIzWnA at least it sparks an interest for more serious discussion to follow.....

    Mar 14, 2012
• Fabio Andrade Machado

  A not-so-new look at epigenetics.

  http://www.cell.com/trends/ecology-evolution/fulltext/S0169-5347%2811%290026 3-1
• Brian Dias

  Looking for N-ChIP protocol for mouse sperm.

  I am looking for a detailed protocol to conduct N-ChIP on mouse sperm (right from collection and then processing). Any ideas? (Preferably not the bare-bones protocols that are published in someI am looking for a detailed protocol to conduct N-ChIP on mouse sperm (right from collection and then processing). Any ideas? (Preferably not the bare-bones protocols that are published in some recent publications). For now, I seem to be losing sample before the lysis step, then when I try and visualize the nuclei after lysis using Trypan Blue (probably not the best stain), I have no idea what i should expect to see. I definitely do not see bodies like the nuclei i see when i work on other samples (eg. brain). Also, at this point any protocols that will let me ChIP sperm samples will do. Thank you.
• Azeem Mehmood Butt

  Phyletic retention and evolutionary conservation

  Hi all, What is the difference between Phyletic retention and evolutionary conservation? Is there any or both represent same thing?

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  • 
    Jeffrey Boore replied

    BLAST is a tool for quickly searching a large database for similar sequences. BLAST scores are meaningless in terms of phylogeny. There is no substitute for full-length alignments, properBLAST is a tool for quickly searching a large database for similar sequences. BLAST scores are meaningless in terms of phylogeny. There is no substitute for full-length alignments, proper calculations of distances from this, and phylogenetic analysis for understanding orthology and paralogy and the patterns of sequence change.

    Feb 8, 2012
• Sneha Sonkamble

  Epigenetic primer in mung bean for PCR?

  Confusion regarding primers.

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  • 
    Sneha Sonkamble replied

    Hello, i'hv gone trough the paper you have suggested me. Thank you for helping me out,regarding techniques of epigenetics.

    Jan 18, 2012
• Aniruddha Chatterjee

  Next generation sequencing

  I am working on next generation sequencing for DNA methylation analysis.. is anyone out there working in similar field.. would like to share views and ideas..

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  • 
    Mukesh Verma replied

    Ya, u can discus with us.

    Dec 28, 2011
• Hong Qi

  Hypomethylation in tumor。。。。

  the expression of proteins which maintain the DNA methylation in tumors is higher than normal tissues ,e.g. UHRF&DNMT1. However, the whole genome is hypomethylated in the tumors. I wonder to knowthe expression of proteins which maintain the DNA methylation in tumors is higher than normal tissues ,e.g. UHRF&DNMT1. However, the whole genome is hypomethylated in the tumors. I wonder to know why? May i check the expression of some DNA demethylase in tissues, such as TET-1,TET-2 and TET-3? Thus, how can I compare the expression of UHRF1-DMNT1 and TET? It's a tough problem.

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  • 
    Shicheng Guo replied

    Martin is right. there are cancer-specific methylation and age related methylation, tissue specfic gene,and some other specific gene I have list them in my blog, you can make some reference

    Dec 6, 2011