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Forum: Vendor Forum 04-07-2011, 05:59 AM
Replies: 10
Views: 9,846
Posted By link1
Does the PCR Free kit use the same adapter DNA...

Does the PCR Free kit use the same adapter DNA ligation technology as the regular NEXTflex kit ? We have been pleased with the ligation in that kit.
Forum: Vendor Forum 04-03-2011, 07:14 PM
Replies: 10
Views: 9,846
Posted By link1
barcodes with PCR free prep

We are very interested in amplification free library prep. We are currently using your Nextflex library prep kit. Can we still use all 48 Nextflex barcodes with the the new amplification free...
Forum: Illumina/Solexa 08-30-2010, 06:11 PM
Replies: 7
Views: 23,426
Posted By link1
in terms of ligation based barcode bias it does...

in terms of ligation based barcode bias it does matter where the barcode is. Adding the barcode to the 5' adapter is not a good idea because the RNA ligase 1 enzyme at this end will prefer some bases...
Forum: Bioinformatics 08-12-2010, 07:17 PM
Replies: 12
Views: 4,056
Posted By link1
agreed gsmapper

agreed gsmapper
Forum: Metagenomics 08-12-2010, 07:09 PM
Replies: 1
Views: 2,228
Posted By link1
filtering samples

has anyone used any other method for extracting dna samples from liquid environmental samples other than filters ?

how about soil?
Forum: Sample Prep / Library Generation 08-12-2010, 07:08 PM
Replies: 1
Views: 2,725
Posted By link1
mag beads?

any recommendations on oligo dT magnetic beads for mRNA pulldown?
Forum: Sample Prep / Library Generation 08-12-2010, 06:58 PM
Replies: 0
Views: 2,320
Posted By link1
mrna seq or directional mrna seq

has anyone tried both of the protocols? any results, any preferences?
Forum: Illumina/Solexa 08-12-2010, 06:56 PM
Replies: 3
Views: 5,425
Posted By link1
sounds like your sample might be lacking small...

sounds like your sample might be lacking small RNA? I would recommend running your sample on a small agilent chip:
http://www.chem.agilent.com/Library/usermanuals/Public/G2938-90092_QSG_smallRNA.pdf...
Forum: Illumina/Solexa 08-09-2010, 07:36 PM
Replies: 7
Views: 3,661
Posted By link1
yes, the 5' adapter should be RNA, otherwise it...

yes, the 5' adapter should be RNA, otherwise it won't work.
Forum: Illumina/Solexa 08-09-2010, 07:25 PM
Replies: 7
Views: 23,426
Posted By link1
multiplex small RNAs

We are multiplexing an average of 8 microRNAs per lane using this strategy :
...
Forum: Illumina/Solexa 08-04-2010, 08:46 PM
Replies: 4
Views: 3,778
Posted By link1
barcoding small RNAs

we tried barcoding the 5'RNA adapter and found significant bias in our small RNA preps. it turns out that RNA Lig I prefers some bases over others. You will need to barcode the 3' adenylated adapter...
Forum: Illumina/Solexa 07-27-2010, 07:37 PM
Replies: 3
Views: 2,015
Posted By link1
if you use an adenylated 3' adapter you don't...

if you use an adenylated 3' adapter you don't have to perform the small RNA gels and cuts. the adapter specifically will bind to your smalls.
Forum: Illumina/Solexa 07-27-2010, 07:34 PM
Replies: 19
Views: 12,538
Posted By link1
small mirna protocol

westlook, not sure what that sequence is....screened my results, haven't seen it.

for the other folks in the forum, I've gotten the miRNA protocol to work consistently now (30th library today)....
Forum: Illumina/Solexa 06-15-2010, 06:48 PM
Replies: 7
Views: 3,661
Posted By link1
the sequences of the adapters and primers for...

the sequences of the adapters and primers for directional mRNA seq are the same as you would use for small RNA library prep. I know the adenylated adapter is DNA.
Forum: RNA Sequencing 06-15-2010, 06:14 PM
Replies: 4
Views: 3,095
Posted By link1
We isolate our miRNA before preparing libraries....

We isolate our miRNA before preparing libraries. You can use any small RNA isolation reagent on the market. Trying to do it with an acrylamide gel is probably too difficult.
Forum: Illumina/Solexa 06-13-2010, 08:18 AM
Replies: 10
Views: 9,815
Posted By link1
thanks Das, thats good to hear. I'm going to try...

thanks Das, thats good to hear. I'm going to try both protocols next week. Will let everyone know how it goes.
Forum: RNA Sequencing 06-13-2010, 08:16 AM
Replies: 4
Views: 3,095
Posted By link1
We've been using the Bioo AIR small RNA Seq kit...

We've been using the Bioo AIR small RNA Seq kit and have been very happy with it. Significantly less adapter dimers in our sequence runs with this kit compared to v1.5, not to mentioned that the Bioo...
Forum: Illumina/Solexa 06-12-2010, 07:35 PM
Replies: 3
Views: 2,260
Posted By link1
I'm gonna try both protocols next week and will...

I'm gonna try both protocols next week and will let everyone know how it goes,
Forum: Illumina/Solexa 06-12-2010, 07:33 PM
Replies: 10
Views: 9,815
Posted By link1
any advice on which one works better? mRNAseq or...

any advice on which one works better? mRNAseq or directional protocol?
Forum: Illumina/Solexa 06-12-2010, 07:30 PM
Replies: 28
Views: 13,099
Posted By link1
advantages to mRNA seq

Does anyone have any results or new results using this protocol...
Any other advantages of this than regular mRNA seq?
Forum: Illumina/Solexa 05-27-2010, 05:42 PM
Replies: 7
Views: 8,444
Posted By link1
hi, the 3' adapter sequence for small RNA...

hi,
the 3' adapter sequence for small RNA sequencing, v1.5 is ATCTCGTATGCCGTCTTCTGCTTG. You'll need it to be 5'adenylated and 3'ddC blocked. You are right the 3' ligation does not require ATP and...
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