Questions tagged [chip]

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 DNA-binding proteins, and studying the sequences and/or epigenetic markers of the DNA.

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Questions about ChIP-seq reads and MACS

I had a few questions raised by the below diagram in relation to how ChIP-seq reads look like (source). I would be very grateful for your insight on them! From the below diagram, it seems that, in a ...
algebroo's user avatar
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What are the effects of buffer on genomic DNA shearing by sonication?

Expt: I have isolated genomic DNA from LNCaP cells and would like to crosslink a small molecule (Chem-seq) to the DNA. The small molecule is an alkylator so it will crosslink DNA on its own. The ...
PaFi's user avatar
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How to design a ChIP-exo experiment with controls?

Does anyone have any ideas on how to run a control/input sample for a ChIP-exo experiment? Is it even necessary to run a control (similar to input DNA for ChIP-seq)? I'm looking for any references ...
PaFi's user avatar
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2 votes
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Interpreting ChIP-qPCR or ChIP-seq

I have a really basic question. Studying ChIP coupled with q-PCR or sequencing, I see different levels of a certain protein among a genomic region. I cannot really understand how can we have different ...
Panagiotis's user avatar
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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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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 ...
masfenix's user avatar
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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 ...
charbot's user avatar
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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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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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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 ...
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