ChIP, or Chromatin ImmunoPrecipitation, is a molecular biology technique used to study protein-DNA interactions in the natural context of the cell. It is performed by cross-linking proteins and DNA, cleaving the chromatin into short strands, enriching for certain regions using antibodies specific to ...

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ChIP-seq for histone modification not in agreement with RNA-seq for expression

I have ChIP-seq for H3K79me2 and H3K36me3 and RNA-seq data for treated and untreated samples. Those two histones mark active genes. Lets say, hypothetically, a peak caller finds differential sites at ...
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What does it mean a “H4K20me1 has a diffuse profile”?

From the paper: H2A.Z is representative of localized signals. H4K20me1 shows the typical behavior of chromatin modifications with a diffuse profile. What does it mean a 'diffuse profile'? Does ...
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Peak calling for TF and histone modification

I was viewing different methods for peak calling and came across two quite similar concepts but still different methods: MACS and SICER. The main difference is that SICER uses nonoverlapping sliding ...
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2answers
418 views

introduction to Chip Seq

I hope this question is suitable for this site. I am concerned about the Chip experiment part so I think it should be okay. I am a Applied Math student starting to get into bioinformatics and so I've ...
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0answers
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Is it reasonable to assume that RNA polymerase would bind preferentially to the promoter of the long allele of the SERT gene?

I'm trying to come up with an idea for a school project (a hypothetical research study). I'm looking at depression and the serotonin transporter gene, which is highly expressed in the human ...
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1answer
317 views

ChIP-seq and the output of SPP

I have been processing some ChIP-seq data with the R package spp. I looked through the literature (ENCODE uses it) and it seemed that spp is indicated as a good program to use. I have found and ...
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74 views

Is it possible to do chip-seq on a specfic region?

Is it possible to do Chip-Seq on specific region of the genome. The idea is to enrich before the sequencing step to have more sensitivity.
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605 views

ChIP-seq vs ChIP-exo

I'm currently investigating ChIP-seq vs. ChIP-exo for finding binding sites. As far as I can tell, ChIP-exo seems to be better in every way than ChIP-seq... but then again, I'm not strong in this ...