Sequencing of PCR products
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Nico B.
Nov 21, 2016, 1:18:41 PM11/21/16
to DIYbio
Hi,
I'm looking into sequencing 4 overlapping mtDNA sites for an art project, none of which exceeding ~522bp. The idea is to collect mtDNA from 10-100 people (depending on seq. costs) in the US all representing different parts of the political spectrum, run sequencing on the HVR1, HVR2 and HVR3 genes (Primers 1, 2, 3a,3b: 522bp, 422bp, 478bp, 261bp) (http://sci-hub.cc/10.1111/j.1537-2995.2006.00775.x#), then compile the data in some TBD visual format to emphasize that we're 99.5ish% (wiki) similar, have more in common than we actively think about, some sort of tag line of 'science and knowledge can remove our barriers of ignorance and emotional justification', and that we need to come together, appreciate similarities and work through differences as a species in times where we're off our rocker because maybe fascism.
I dont know very much about types of sequencing (so far read a little bit on sanger, single-end, pair-end seq) but not sure what would be best for accuracy, what would be most cost effective, etc. I would love some direction when it comes to types of sequencing, costs, and services. I'm very much open to collaborations on hardware/visualization folks, as well as working together with hackerspaces across the country to generate as much of this data as possible.
Best,
Nico
I'm looking into sequencing 4 overlapping mtDNA sites for an art project, none of which exceeding ~522bp. The idea is to collect mtDNA from 10-100 people (depending on seq. costs) in the US all representing different parts of the political spectrum, run sequencing on the HVR1, HVR2 and HVR3 genes (Primers 1, 2, 3a,3b: 522bp, 422bp, 478bp, 261bp) (http://sci-hub.cc/10.1111/j.1537-2995.2006.00775.x#), then compile the data in some TBD visual format to emphasize that we're 99.5ish% (wiki) similar, have more in common than we actively think about, some sort of tag line of 'science and knowledge can remove our barriers of ignorance and emotional justification', and that we need to come together, appreciate similarities and work through differences as a species in times where we're off our rocker because maybe fascism.
I dont know very much about types of sequencing (so far read a little bit on sanger, single-end, pair-end seq) but not sure what would be best for accuracy, what would be most cost effective, etc. I would love some direction when it comes to types of sequencing, costs, and services. I'm very much open to collaborations on hardware/visualization folks, as well as working together with hackerspaces across the country to generate as much of this data as possible.
Best,
Nico
Sebastian S Cocioba
Nov 21, 2016, 2:16:40 PM11/21/16
to diy...@googlegroups.com
Send out purified PCR products to GeneScript, pay by PO Number/ Check and they cut the cost in half. Bout $3/read up to 1200bp (usually 700bp+ if bands are bright) using good old Sanger sequencing. Or for a bit more they can just take your pcr tubes raw as long as you provide an aliquot of each sample. Thats $5 per read (two reads per amplicon (fwd and rev)). I use genewiz personally. They are in new jersey so its super quick turn around and in an emergency i can just drive to their site and drop off.
Sebastian S. Cocioba
Sebastian S. Cocioba
CEO & Founder
New York Botanics, LLC
Blog: ATinyGreenCell.com
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Nico B.
Nov 22, 2016, 7:20:10 PM11/22/16
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Awesome! thanks for the info, Sebastian!
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