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christophertbrown / iRep

scripts for estimating bacteria replication rates based on population genome copy number variation
MIT License
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Enquiry on application of IREP to my experiments #34

Open samkjm opened 4 years ago

samkjm commented 4 years ago

Hi

This is not really an issue but just an enquiry.

I am a biologist and I am trying to find out more about the applications of iREP to my experiments, not much on the detailed codes itself. The way the downstream analysis would be run would affect my actual experimental workflow.

I am trying to do a coculture of bacteria where one can potentially kill the other without lysis. I would be collecting cell pellets in a time course experiment of the 2 bacteria grown together. After which i would extract the coculture pellet and subject it to illumina sequencing. iREP can potentially be used but would iREP capture this killing effect? for e.g if Bacteria A is highly replicating, and Bacteria B starts killing A at some point at a time when A is highly replicating, the iREP values may still be relatively high is it?

Thank you!

Rgds Samantha

christophertbrown commented 4 years ago

Hi Samantha,

You bring up a very important point with your questioning: cell replication and death are not necessarily linked. That being said, I think iRep could still be an interesting metric to collect in your experiment. Knowing whether or not the culture conditions are halting replication or killing cells in some other way could be useful. Given that this is a two bacteria co-culture, it would be helpful to look at relative abundance data from DNA sequencing, along with some other quantitative metric (such as cell counts or total amount of DNA) in order to be able to tell when one (or both) cell populations are changing.

Hope this helps.

Best,

Chris

On Aug 2, 2020, at 7:46 PM, samkjm notifications@github.com wrote:

 Hi

This is not really an issue but just an enquiry.

I am a biologist and I am trying to find out more about the applications of iREP to my experiments, not much on the detailed codes itself. The way the downstream analysis would be run would affect my actual experimental workflow.

I am trying to do a coculture of bacteria where one can potentially kill the other without lysis. I would be collecting cell pellets in a time course experiment of the 2 bacteria grown together. After which i would extract the coculture pellet and subject it to illumina sequencing. iREP can potentially be used but would iREP capture this killing effect? for e.g if Bacteria A is highly replicating, and Bacteria B starts killing A at some point at a time when A is highly replicating, the iREP values may still be relatively high is it?

Thank you!

Rgds Samantha

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