Flow cell/channel terminology

[Calico]

Hello all,

I am a little bit perplexed of the exact mening of the term 'channel' as it is used by Helicos. So, I understand that there machine has two flow cells - in one the synthesis reaction takes place whilst the other is being imaged and this switches back and forth for each added nucleotide. However, each flow cell has 25 independent channels; what does that mean? Does each channel correspond to a picture like this one? Basically, if the HeliScope was a qPCR machine, would it correspond to it being able to run two multiwell plates at the time, with 25 wells per plate?

Edit: Just found a footnote in their product specification sheet stating that for more than 50 samples multiplexing or barcoding is required. This would mean that I am right, right?

[Xi Wang]

I think you are right that each channel is a independent picture for a scanner to photo. So it is similar with illumina GAs.

[krobison]

Looking at the image on the Helicos website may help you -- though I'd suggest any future photographers of these load them up with colored dye to get some higher contrast. Each channel is more than a separate area to photograph, but is an actual separately microfabricated liquid holding region.

[Xi Wang]

Sorry I mixed something up. Channel for Helicos may equal to Lane for Illumina.

[Calico]

Allright, that photo at least clarifies why they call them channels (i.e. they are channels). Though, now I am uncertain what the picture I posted is - a whole flow cell or a segment of a single channel?

[Xi Wang]

illumina calls that small square tile. a channel (lane) is made up by several (120 for illunima, 60 rows X 2 cols) tiles.

[Calico]

And that would be the case for Helicos as well?
Are they imaged sequentially or all simultaneously (in that case, all ties of one channel or of one flow cell at the same time)?

[Xi Wang]

sorry, my typo, it's tile, not tie.
they are imaged sequentially. and it is the most time consuming step.