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I've got a short question. Does anybody know the chemical components of DNA capture beads? Thought that I read something about agarose, but I can't find it now.
Thanks
Thanks
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Last edited by Christine90; 12-27-2012, 11:43 AM. -
If you're talking about the white DNA beads, they're polystyrine if I remember right. It might say that in a manual somewhere, but I'm not sure where. I just remember learning that from a 454 person somewhere along the line. -
The composition of beads is different now from what described in the original paper. I tried to make my own beads and used beads from several vendors, including crosslinked agarose as in the paper. Adarose beads are not even close in appearance of the current beads, so are polystyrene beads. The closest I found are beads from Tosoh Biosciences, they even offer carboxylate beads, which look exactly as the current capture beads. However, any kind of beads can be used, the issue is to introduce sufficient density of carboxyl groups and go through a very tedious procedure of narrow size selection, which is not an easy task as size selection materials are not easily available. Carboxyl groups are used to attach capture oligo.
I am doing this as it may be a time to start thinking about home-made reagents as 454 eventually may decide to drop this production line. No reason for panic yet as a lot sequencers are still in use, but tech support and programmatic help seem to slow down significantly. I had to abandon GS Jr ver2.7 gsMapper and gsAssembler and turn back to 2.5p1 as the problems with 2.7 had not been fixed after bugging them for six (!) months. While I think I figured out how to make capture beads and how to concoct emulsion oil recipe, I am not clear about sequencing reagents though, as Titanium reagents differ from what was published.Last edited by yaximik; 12-28-2012, 07:43 AM.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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