How much sequencing output for chip-seq?

[DNA Sorcerer]

How much reads/bp are typically aimed for in a chip-seq experiment? Do people run one lane of GAII for one experiment? Is that more than enough?

thanks

[captainentropy]

How much reads/bp are typically aimed for in a chip-seq experiment? Do people run one lane of GAII for one experiment? Is that more than enough?

thanks

That's not an easy question to answer. It depends on many variables. The first being - what organism are you using? One could easily reach saturation for a ChIP target or input control in a single GAII lane with say, yeast or Drosophila as your target. Human and mouse, probably for the ChIP but certainly not the input control. It also depends on the target. If you're ChIPing histones, there are millions of "binding" sites whereas a transcription factor might have 10,000. For most experiments one lane is likely enough but I know one major sequencing center will multiplex all their samples and load them over several lanes to control for lane-to-lane variations in Illumina flowcells.

I suggest you first read these two papers to get an idea of sequencing depth and other issues.

Design and analysis of ChIP-seq experiments for DNA-binding proteins - http://www.ncbi.nlm.nih.gov/pubmed/19029915

excerpt:

In practical terms...lack of saturation point has profound implications in study design. It suggests that it would be difficult to define a 'sufficient' depth of sequencing and that other criteria must be specified.

We therefore propose that the sequencing depth requirements should be evaluated with respect to a specific target enrichment ratio of the binding positions.

PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls - http://www.ncbi.nlm.nih.gov/pubmed/19122651. Pay attention to Figure 5.

(also your thread might get more visibility in another forum topic - I'm not sure how relevant this is to RNA-seq)

good luck!

[DNA Sorcerer]

Thank you captain. Very useful tips indeed, will read those papers.


Regards,