which one would be the better way for RNA-seq Experiment design
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9.8 years ago
Manvendra Singh ★ 2.2k

I have a few questions concerning RNAseq experiment.

we have 10 samples, 5 controls vs 5 Patients. We are going to run them into two lanes. I am wondering how should I index and pool them. Should I use 10 different indexes, pool them all and run in two lanes (that will makes two replicates) or to use 10 different indexes but pull 5 samples in one lane and 5 samples in the second lane that we will have in each pool as different indexes as possible, if so should I run 5 controls in one line and 5 cases in the second line or combine them i.e. 3 controls + 2 cases in one line and 2 controls + 3 cases in the second one.

I hope it is understandable what I wrote.

Thank you in advance.

RNA-Seq • 2.3k views
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9.8 years ago
User 59 13k

10 plex them and put them down two lanes (i.e. all ten samples in BOTH lanes). This means you will not get any lane to lane biases. And if you have a lane failure, you'll still have a lane of usable data! If you have two good lanes, then you can combine the data and run it as the 5v5 comparison from your 20 outputs.

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Thanks Daniel, I would do it in the same way!


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