Illumina V3 vs. V4 chemistry

[buthercup_ch]

Hello everyone.

We are dealing with RNA-Seq of bacteria.
So far, we were using HiSeq2000/2500... with V3 chemistry. But recently the genomic platform has the HiSeq4000 available... which runs with V4 chemistry.

Can anyone explain me briefly what is the difference between both chemistries?
Can V4 be used in HiSeq2000?

Thank you ni advance

[Jessica_L]

The HiSeq 4000 has its own set of cluster kits and sequencing reagents, from what I can tell. See page 2 here for run specs:

http://www.illumina.com/content/dam/illumina-marketing/documents/products/datasheets/hiseq-3000-4000-specification-sheet-770-2014-057.pdf

You'll get ~2 billion reads per flow cell, give or take, going up to about 2.5billion. The v4 chemistry on the HiSeq 2500 appears to have 2 billion reads per flow cell as the upper limit. See here:

http://www.illumina.com/systems/hiseq_2500_1500/performance_specifications.html

The cluster kits have different part numbers in the Illumina catalog, so there are probably differences in things like the flow cells used on the instruments. Off the top of my head, and please, anyone correct me if I'm wrong, I think the HiSeq 2000 only works with v3 chemistry. The 2500 instrument is required to run the v4 chemistry as the flow cell is different which required an optics change/upgrade that isn't compatible with the 2000 hardware. I'm a bit out of the loop on the HiSeq series now, so take what I say with a grain of salt.

To be honest, if you have specific questions about running something like v4 chemistry on a HiSeq 2000, you really would be better off contacting Illumina tech support as they would know all the relevant information on your instrument-- what optics/lasers/flow cell stage you have and what labware/reagents that is compatible with.

[GenoMax]

As indicated on this page only those machines with serial numbers meeting condition below can take advantage of the V4 upgrade.

HiSeq 2500 SN# D00101 or higher

HiSeq 2000 SN# 7001403 or higher