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Choosing the right sample among GEO datasets

Hello,

I am trying to create a pool from MCF7 cell line samples targeting only one specific transcription factor. I think we can say that I will proceed with them like they are biologiclal replicates. I need to obtain non targeting, or samples treated in the same way but with no specific treatment. But I got confused in two ways.

1) Can I pool vehicle samples with DMSO and DSG (these are examples, it could be ETOH, DMEM, etc.) treatment together?

2) In one sample for example it is only written "MCF7", in the other one ; "MCF7, .... tissue" what does that mean in terms of the experiment and again can I pool them together in order to proceed as they are biological replicates.

As I know, "biological replicate" should be another experimental set up under the exact same conditions. But I almost could not find the exact same ones.

Thank yoy in advance.

geodatasets chipsamples celllinesamples chipseq chipseqanalysis
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updated by ATpoint ATpoint • written by buffealo • buffealo

I think we can say that I will proceed with them like they are biologiclal replicates

It is almost certain that batch effects will completely dominate any analysis you will do on these pseudo-biological replicates. You most likely will not get any meaningful results from pooling independent experiments. Can you describe what the analysis goal is?

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written by ATpoint ATpoint

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