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Flow cells
Wondering if anyone knows of platforms using silicon based flow cells? Only in electrical detection or also examples of fluorescence based detection using silicon flow cells? Thanks!!
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If you are referring to silicon (SiO2) <--> glass then Illumina is the best known platform. I am reasonably certain that the zero mode waveguides in PacBio SMRT cell have glass at the bottom of the well (since the detection is done by shining a laser through the bottom of the well). -
@GenoMax How do the flow cells from Illumina work? The wells and primers are etched on the silicon side and the glass side is where the laser excited the fluorofores and the lens measures the emission? I can't find on the Illumina website that the wells are etched on silicon, they only seem to mention glass. Thank you!Comment
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The exact process/materials used for the flowcells is probably a trade secret but every flowcell I have looked at appears to be made of excellent quality/optically clear (at least the lane part) glass (never tried to break a flowcell).
Illumina has a number of videos on youtube that superficially describe how the flow cells work.
Illumina has thousands of patents related to flowcells and this one mentions the surface being silicon, glass and plastic.
Ultimately Silica is going to be major component of all "glass" (https://en.wikipedia.org/wiki/Silicon_dioxide).Comment
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@GenoMax, you seem to be knowing a lot...
It indeed seems to be a bit of a trade secret. The patent mentions "wherein the transparent regions comprise glass, plastic OR silica". From my understanding all flow cells on the market use glass for at least the transparent region/the side where excitation/emission takes place. Although technically silicon or plastic could be used if the right optical density.
It seems that Illumina uses glass for the top part of the flow cell but unclear to me what the bottom part is made off, where the wells are etched and the primers attached. My guess is based on the patent that it's glass coated with polymers, what do you think? So maybe not silicon?
In general for pattered flow cells would the pattern be etched on silicon or can it also be glass, I guess it can be both after the glass is coated with something? Not sure what the pros and cons of each are. Silicon is probably easier to manipulate and glass might be cheaper? Any thoughts on this?Comment
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Non-patterned flowcells are imaged both from top and bottom so both surfaces are likely made of glass (I am no materials scientist but they do seem to be like glass).
YouTube video says that the nanowells are etched into glass (if that is accurate) for patterned flowcells.Comment
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Very interesting. Are there still any non-patterned flow cells on the market? It seems that Illumina now completely move to patterned flow cells.Comment
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Only Illumina can say exactly what percent but patterned cells are likely only a fraction of the total. They may be for a long while.Comment
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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...
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