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Old 12-22-2010, 02:28 PM   #1
BIG_SNP
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Default TruSeq adapter sequences?

Does anyone know the sequences for the new TruSeq adapters?

Thanks!
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Old 12-23-2010, 10:30 AM   #2
EdibleMetal
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The new TruSeq adapters for DNA library prep are 60 bp/side (rather than 32 bp/side). I'm not sure how many bp PCR adds to that in the new prep, and Illumina doesn't plan to release any of these sequences until sometime next year. I figure someone will end up sequencing the adapters before Illumina officially releases the sequence.
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Old 01-12-2011, 04:54 AM   #3
SeqTruth
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In case this is of interest to anyone, I believe I have most of the TruSeq index sequences:

I stumbled on a screenshot in one of their tech bulletins that confirmed some preliminary sequence information we have; the indexes appear to be as follows:

TruSeq Indexes (?)

1 ATCACG
2 CGATGT
3
4 TGACCA
5 ACAGTG
6 GCCAAT
7 CAGATC
8 ACTTGA
9 GATCAG
10
11
12 CTTGTA

I would also be very interested in the full TruSeq adaptor oligo sequences.
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Old 01-19-2011, 05:12 PM   #4
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TruSeq adapter sequences posted in this thread were removed by request, please see the statement below from Illumina.

Quote:
"For the past few years, Illumina, Inc. has made sequence information used in its sequencing technology available to customers upon request. This information is frequently updated and subject to certain restrictions. For more information, please contact Illumina Customer Solutions at 858-202-4566 or [email protected]"
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Old 01-19-2011, 07:35 PM   #5
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We just recevied the full TruSeq sequences from our FAS so I imagine that they are available from Illumina based on their terms and conditions. Just as an FYI, the sequences are exactly the same as the previously published multiplex sequences except that, as noted above, the ligated adaptors are complete and PCR is optional.

The sequences will be a bit more challenging to make and when you consider the longer length and the price reductions for the new kits, the advantages of making them in the lab are greatly diminished.

The available 48 index sequences are also available. 12 are in the TruSeq RNA kit and the other 36 are in the small RNA kit. There was an error in indexes 25 and 26 being the same, but I think that has been fixed in the current documents.
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Old 01-20-2011, 04:49 AM   #6
krobison
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The key bit that Illumina needs to publicize is what you need to design into PCR primers to create what 454 calls "fusion primers". With the 2x150 format & the fast times on the MiSeq, direct amplicon sequencing on Illumina will become common -- but only if folks can design the primers!!
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Old 01-20-2011, 07:14 AM   #7
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Attached is a list of all their barcodes

TruSeq kit A contains index numbers 2,4,5,6,7,12 and should be used when pooling 6 or fewer samples together.

TruSeq kit B contains index numbers 1,3,8,9,10,11.
Attached Files
File Type: pdf TruSeq index sequences-3.pdf (27.7 KB, 2965 views)
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Old 01-25-2011, 02:06 PM   #8
ECO
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NGS,

Illumina has asked that I take down any TruSeq Adapter information. See their statement above. Apologies but I can't take them on!

Eric
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Old 04-07-2011, 11:16 PM   #9
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Hi There...... I am in desperate need of the Truseq adapters and other Truseq sequences.... From what I understand is that some one had already posted the Truseq sequences in the Thread but they have been removed probably because of the Proprietory issues... if anyone does know something about those sequences, Kindly help me out wth this bit of Information.....I am using the Truseq kits, as they are all upgraded... Because I cant make the libraries blindly.... I need to know what adapters I am using and what happens in the downstream process of sequencing.......I feel the admin will reject the post if it includes Truseq sequences.... If that is the problem, Kindly send me a personal message to my mail ID..... Regards.....SPS
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Old 04-18-2011, 04:58 AM   #10
james hadfield
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Hi Santosh,

Just contact Illumina's techsupport team and ask. They give them out freely but there are restrictions on redistribution. It appears heavy handed but at least you know the data you are sent are up-to-date.

Illumina Technical Support <[email protected]>
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Old 04-19-2011, 07:04 AM   #11
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Illumina will give out the adapter sequences but they refuse to give out the sequences of the sequencing primers. It's like pulling teeth to find out what the HP7 primers are.
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Old 04-19-2011, 07:35 AM   #12
james hadfield
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The Genomic DNA Sequencing Primer is given on page 6 of the latest primer sequence document from Illumina. This is the same for most applications and a simple search in the PDF will show you where this sequence binds to other adapter molecules.
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Old 04-19-2011, 08:28 AM   #13
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What are the HP7 turn around primers though? Apparently it is a mixture of PE Read 2 and Multiplex Read 2 but they won't confirm this.
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Old 05-03-2011, 07:43 PM   #14
aniruddha.otago
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Hi All,

I am preparing libraries for methylation sequencing using the true-seq kit. I will do bisulphite conversion after size selection. Can anyone tell me the how to get / to design the primers to amplify the library after bisulphite conversion. I have confirmed from the Illumina tech support guys that the adaptors are methylated, so bisulphite conversion will not have any effect on the adaptor sequences.

Can anyone help with details , please.

- Aniruddha ([email protected])
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Old 06-08-2011, 01:45 AM   #15
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We are using TruSeq kits and currently only 12 different index sequences are available. I was already wondering when more would be released.
Now I see in the PDF-file that was attached above that for Small RNA libraries, there are 48 sequences. Does anyone know if they will ever be available for cDNA / gDNA etc.?
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Old 06-08-2011, 06:35 AM   #16
NextGenSeq
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Bioo Scientific has a kit with 48 barcodes that's available now.
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Old 06-08-2011, 06:50 AM   #17
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Hi All,
Has anyone made directional libraries from bacterial mRNA using Truseq small RNA adapters? Any information on this will be helpful

Thanks
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Old 06-28-2011, 09:58 PM   #18
kaiman
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Default Truseq genomic library

I have problems with the Truseq library kit. Some of my libraries work, some don't. I did size selection on e-gel and have very good gel recovery. However, some of the PCR didn't work. These libraries use different index adapters. Is it an index related ligation problem?

If you have experience with truseq genomic library kit, please share the experience with me.

Thanks
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Old 06-28-2011, 11:27 PM   #19
ETHANol
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I don't personally have any expertise in regards to your question, but take a look at this thread. Seems some other people have had problems with e-gels and TruSeq.
http://seqanswers.com/forums/showthread.php?t=9124
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Old 08-19-2011, 02:14 PM   #20
Howie Goodell
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A bioinformatics question with chemistry inputs: I am trying to convert RNAseq cDNA Bioanalyzer read sizes to the correct TopHat read spacing (-r parameter). I used to subtract the sum of the lengths of the Illumina Paired-End adapters plus the sum of the number of bases read to get the read separation (negative if there's overlap). I'm trying to figure out how this should be adjusted now that we are using the TrueSeq kits with multiplexed adapters. I have their sequences, but I'm not sure exactly what's on each end of the molecule when it is Bioanalyzed. I know a TruSeq Adapter (all length 64) is ligated on the 5' end. No TruSeq Universal Adapter (length 59) "Y" at that point, right? My main question is what's on the 3' end -- the old PE second read adapter (33 bp), or something else?

Thanks!
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