Questions tagged [chip-seq]

For questions about ChIP-seq (Chromatin ImmunoPrecipitation sequencing), a method used to analyze protein interactions with DNA.

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chip sequencing

I understand the concepts of steps in Chip-seq up to DNA purification, but I don't get how one can then amplify the purified DNA samples that are once bound to the proteins.... Since sequence-specific ...
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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 ...
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Cross correlation metric in ChIP-seq experiments

I found this explanation of cross-correlation metric in ChIP-seq. Now, the definition of Pearson's correlation coefficient between two random variables $X$ and $Y$ is $$\rho_x = \frac{Cov(X,Y)}{\...
algebroo's user avatar
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Can different cell lines of same type symbolise samples from different patients in ChIP-seq?

Can I simulate different patients by using different cell lines of the same cell type and from the same tissue? Can I also study apoptosis in an immortalised cell line? I have a gene X (transcription ...
Charles'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 ...
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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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How to annotate the SwitchGear gene models?

According to this page(http://switchgeargenomics.com/wp-content/uploads/2009/02/switchdb_technote1.pdf), the SwitchGear gene models can be annotated by the NCBI annotation associated with Refseq ...
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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 ...
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How to Download the broadpeak files from the encode chip-seq experiment matrix? [closed]

I have tried the SqlDatabase of Encode opened it trough R ,i have tried other packages in R, i have tried the ENCODExplorer package but none of them seems to do what i want. I have an app that asks ...
Xanthoula Atsalaki's user avatar
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How to annotate a .broadpeak file with 9 columns?

I have this peak file I retrieved from an ENCODE chip-seq matrix. Its .broadpeak file looks like this: ...
Xanthoula Atsalaki's user avatar
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ChIP-seq data Analysis Database

Where can i find already analyzed ChIP-Seq Data? Is there any database or any web tool that takes ChIP-seq raw data and automatically analyzes them? Or is there any database that provides some API to ...
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Summarising ChIP-seq and controls needed

As part of my study I have to present on a method of discerning binding sites of proteins to DNA, for which I have looked at ChIP-seq. This is a brief overview of what I have so far, and was wondering ...
user19450's user avatar
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No genes' ID in peak annotations during ChiP-Seq with ChIPpeakAnno R package

I am trying to perfom Chip-Seq Analysis which is greatly described in that conversation: introduction to Chip Seq . The same as autor of mentioned question I am a student of Applied Mathematics and I ...
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How is magnet based bead capture used for indexing-first ChIP-seq?

The context for this question can be found in this paper by Lara-Astiaso et al. Here, to study H3K4 trimethylation in various cell types, they sort cells sonicate chromatin immobilize chromatin on ...
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