solexa genomic adapter and pictures?

[ECO]

Yup. In this thread when they were posted initially, I received a very nice email from their Senior Patent Counsel. Post#4 in that thread has the statement ILMN asked me to include with the takedown.

I hadn't seen that release above...the original posting did have that copyright attached as I remember.

[ScottC]

You have to ask Illumina for them. I posted a pdf of them but Illumina made this site take them down.

Hi guys/ScottC,
NextGenSeq is correct, ILMN does not want the TruSeq adapter sequences published here.
Apologies...

Really? You were actually told by Illumina to remove them? Why would they care? It was sent to me out of the blue by Illumina staff, I didn't request it. They told me to feel free to distribute it.

You're certainly allowed to publish 'individual sequences'...

"For individual sequences contained in this letter, lllumina grants you permission to distribute them outside your institution, or publish individual sequences in presentations, manuscripts, or publications authored by you, as long as it is accompanied by the following copyright notice:
Oligonucleotide sequences © 2007‐2011 Illumina, Inc. All rights reserved."

[ECO]

Hi guys/ScottC,

NextGenSeq is correct, ILMN does not want the TruSeq adapter sequences published here.

Apologies...

[NextGenSeq]

You have to ask Illumina for them. I posted a pdf of them but Illumina made this site take them down.

[genlyai]

Thanks, Scott.

What I'm confused about is the PCR primers that are used with the TruSeq DNA and RNA adapters. Can you (or someone) clarify what those are?

[protist]

I have same question.

I have attached a figure I use as an explanation - hope it helps.

[marcaill]

Thanks Protist.
That's what we understood too. The ultimate goal would be indeed to avoid PCR step.
I'm looking forward adapters sequences for confirmation...

[protist]

Does anyone have explicit, detailed information about the new TruSeq adaptor sequences and structures?

In an Illumina webinar yesterday it was stated that they are equivalent to 'complete adapters' ie., they have the extension which is normally added during the library amplification that allows the library material to anneal to the Flowcell. Thus if you start with enough material you could potentially skip the Library amplification step.

See paper below for discussion of 'complete adapters'
Nature Methods 6, 291 - 295 (2009) Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes

[huqiuping]

I have same question.

Hi,

I am a little confused with the various schematics I found on the Solexa adapter structure.

I followed Illumina's pdf (attached) and made the forked structure myself (jpeg). I also listed the variations I saw on the right taken from various schematics people have posted on this website which I think they took from other journal articles.

Can someone tell me if the sequences taken from Illumina's pdf are the correct forked structures as I've drawn them, meaning is that the way they're really supposed to look? My version has more bases ligating to each other versus the ones taken from this website which have fewer, why is that and does it make a difference? Thanks.

[SeqTruth]

Does anyone have explicit, detailed information about the new TruSeq adaptor sequences and structures?

[anant]

Thanks kmcarr, it is very useful and information.

[seqgirl123]

need some help

Hi,

I am a little confused with the various schematics I found on the Solexa adapter structure.

I followed Illumina's pdf (attached) and made the forked structure myself (jpeg). I also listed the variations I saw on the right taken from various schematics people have posted on this website which I think they took from other journal articles.

Can someone tell me if the sequences taken from Illumina's pdf are the correct forked structures as I've drawn them, meaning is that the way they're really supposed to look? My version has more bases ligating to each other versus the ones taken from this website which have fewer, why is that and does it make a difference? Thanks.

[Anri]

I want to sequence my PCR product on Solexa (it's a long story). Will it be feasible to PCR amplify with primers that has the Illumina's long PCR primer sequence extended to the 5'end so I don't have to do adaptor ligation again?

Check this article. Is anyone done something like this? (http://www.ncbi.nlm.nih.gov/pmc/arti...ukmss-3213.pdf).

Direct sequencing of short amplicons
To avoid unnecessary PCR amplification steps, which would potentially exacerbate biases, we can perform extremely deep sequencing of short amplicons using locus-specific primers that possess tails that are capable of hybridisation to the oligos tethered to the flowcell surface. The tailless forward and reverse oligos are then used as primers in the sequencing steps
(Supplementary Protocol 10 online).

[abelhj]

Sorry my graphic got messed up. Here it is again.

Hi,

I am trying to figure out Solexa paired end read output. Can someone please tell me if my toy example is correct?

1) One end of DNA is bound to substrate. Free end is sequenced in 5'-->3' direction.

#
5' #
------> #
GCCCxxxxxxATTT # ==> GCCC
CGGGxxxxxxTAAA#
#
#
#

2) Opposite end of DNA bound to substrate. Free end of *complementary* strand sequenced in 5'-->3' direction.

#
5' #
------> #
AAATxxxxxxGGGC# ==> AAAT
TTTAxxxxxxCCCG #
#
#
#

So the final output of the Solexa machine would be the pair (GCCC, AAAT) and then a program such as maq would worry about the details of orientation/taking complements.

Thanks,
hja

[abelhj]

Hi,

I am trying to figure out Solexa paired end read output. Can someone please tell me if my toy example is correct?

1) One end of DNA is bound to substrate. Free end is sequenced in 5'-->3' direction.

#
5' #
------> #
GCCCxxxxxxATTT # ==> GCCC
CGGGxxxxxxTAAA #
#
#
#

2) Opposite end of DNA bound to substrate. Free end of *complementary* strand sequenced in 5'-->3' direction.

#
5' #
------> #
AAATxxxxxxGGGC # ==> AAAT
TTTAxxxxxxCCCG #
#
#
#

So the final output of the Solexa machine would be the pair (GCCC, AAAT) and then a program such as maq would worry about the details of orientation/taking complements.

Thanks,
hja