If you are going to read the plate from the top, you should use a solid black plate. If you are going to read it from the bottom, you should use a clear-bottom black plate (more expensive). If you want to reduce the assay volume to reduce the use of reagents, use a half-area plate.

Polystyrene is a very hydrophobic surface to which things tend to stick, which you want to avoid. If there is detergent in your assay (e.g. 0.005% Triton X-100), it will coat the plate and prevent this from happening. In that case, you can use a plate with untreated surface (sometimes called medium-binding). If you don't have detergent in the assay, or can't put some in, you should use a low-binding plate (Corning sells plates with a "non-binding surface").

Plates can also have flat or round-bottom wells. You can use either one for top-reading, but only flat-bottom ones for bottom-reading.

Black plates can also be made of polypropylene, which tends to have lower binding than polystyrene.

Thank you very much Adam, that is very helpful.

Nisha

you can use 384/96 well clear bottom black plate 

Thank you Mark for the paper. We will go with low binding plates. We have ThioT in hand, so will start with that.

Thank you Richard.

Our instrument can read from top or bottom, so looks like I should be getting a solid black, low binding, round or flat bottom plate. With an assay duration of about 2h, the sterility of the plate should not be a factor right?

In most amyloid aggregation experiments, evaporation becomes a serious concern over the timescale of the experiment, especially if it takes place at elevated temperatures. It is usually necessary to cover the microplate with a clear cover to prevent the solution from evaporating. The microplates are usually read from the bottom because condensation causes scattering if read from the top. 

Detergents will cause serious artifacts in the aggregation assay and I would not recommend their use. 

Obviously, using a totally clear plate will mess it up.

Assay plates (EIA/RIA high-binding flat bottom polystyrene microwell plates) were obtained from Corning/Costar Inc., Corning (New York, USA)used for ELISA.

solid black plates are suitable for fluorescence mesurment.

So what's the pro's and con's of reading from the top or bottom? Is there a difference? Is one way better than the other?

This document provides a nice summary:

https://www.berthold.com/en/bioanalytic/knowledge/magazine/top-vs-bottom-reading/

Hi, following on the thread and hoping someone will still respond.

I do tissue culture adhering cell lines in 6 well plates (transparent ones) typical for tissue culture. So far in the lab MitoSox red assay was done on this cultures with microscopic image acquired but never analysed in the quantitative way.

Is it possible to use stained cells in this type of culture plates to read fluorescence directly by plate reader or same rules will apply as in the previous comments and I should look for black plates?

I can check the plate autofluorescence obviously.

Thanks