Question

What does numbers 5 and 7 in P5 and P7 of illumina adapters signify ?

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3.4 years ago

gsr9999 ▴ 300

Dear BioStar Leaders,

I understand that 5' prime and 3' prime represent the open end of the DNA molecule, i.e. the carbon atom position in the deoxyribose sugar molecule of nucleotide bases(A,T,G,C) and also they help provide the directionality of sequencing.

I know that illumina named the oligo sequences as P5 and P7 that enables adapters to bind to FlowCell in bridge amplification step, where P probably stands for Primer, and my question is why did they choose numbers 5 and 7 ? and what do they mean ?

Similarly, why did they choose numbers 5 and 7 for sample index oligo sequences i5 and i7 ?

Thanks, gsr

next-gen RNA-Seq sequencing sequence rna-seq • 8.2k views

ADD COMMENT • link 3.4 years ago by gsr9999 ▴ 300

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Good question. It may be just a coincidence. I have not heard of a specific provenance for those numbers. It is one of those things that may be written up one day by someone who was originally involved with the invention of solexa chemistry magic. Many still don't realize that p7 indexes = Index 1.

ADD REPLY • link 3.4 years ago by GenoMax 142k

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thank you for the answer @genomax

ADD REPLY • link 3.4 years ago by gsr9999 ▴ 300

score 7 · Accepted Answer · 2020-11-29

Ok, I guess I found the answer for this question from Twitter.

https://twitter.com/kevinwuhoo/status/1291867993475911680 https://twitter.com/Genomics_Guy/status/1292194427771826176

This "Sequencing by Synthesis" technology is acquired by illumina from Solexa, and Solexa acquired some part of this technology from another swiss company 'Manteia'.

It appears like many other primer sequences existed at that times like P1, P2, P3, etc. , and P5 and P7 were the best primer combinations for cluster formation at the time, and they have used them ever since