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Search: Posts Made By: saikumarkv
Forum: Illumina/Solexa 03-28-2012, 02:07 PM
Replies: 6
Views: 6,882
Posted By saikumarkv
Demultiplexing in-line barcodes

Gruberjd: Thanks for the info. I run the sequencing core at University of Cincinnati. Only recently I'm getting into data analysis.
Forum: Illumina/Solexa 03-28-2012, 02:06 PM
Replies: 6
Views: 6,882
Posted By saikumarkv
Demultiplexing in-line barcodes

kmcarr: I used NuGen's Ovation pico kit (older version) that has 4b barcodes. Thanks for the info. I will pass it on to our informatics people. They typically get data from TruSeq library samples....
Forum: Illumina/Solexa 03-26-2012, 01:08 PM
Replies: 6
Views: 6,882
Posted By saikumarkv
HESmith, when I talked to Illumina they said it...

HESmith, when I talked to Illumina they said it cannot handle in-line barcodes. I will check the manual. Thanks
Sai
Forum: Illumina/Solexa 03-26-2012, 10:57 AM
Replies: 6
Views: 6,882
Posted By saikumarkv
Demultiplexing in-line barcodes

Hi all,

I just used a kit that has in-line barcodes for multiplexing RNA-seq samples. CASAVA cannot handle in-line barcodes. Can anyone suggest if there are any other tools and the best way to...
Forum: Sample Prep / Library Generation 02-18-2011, 01:44 PM
Replies: 0
Views: 2,291
Posted By saikumarkv
Lib prep with 10-200bp (45bp peak) gDNA

Hi everyone,
Has anyone made PE lib prep with 10-200bp gDNA. The peak is at 45bp. I'd like to select 25-100bp. I have successfully made a number pf PE libraries with as little as 2.5 ng. I may...
Forum: Illumina/Solexa 12-15-2010, 07:46 AM
Replies: 2
Views: 2,083
Posted By saikumarkv
I tried to respond directly, but your were not...

I tried to respond directly, but your were not accepting emails. Yes the final conc of PE adapters I used for 1ng was 1.67nM.
Sai
Forum: Illumina/Solexa 10-26-2010, 10:34 AM
Replies: 16
Views: 8,663
Posted By saikumarkv
Just finished estimating my library prep using...

Just finished estimating my library prep using the KAPPA qPCR kit. I'm actually estimating more of the library than by Qubit measurement. Using 1 ng of ChIP input DNA I'm getting 37nM by Qubit and...
Forum: Illumina/Solexa 10-21-2010, 01:05 PM
Replies: 16
Views: 8,663
Posted By saikumarkv
I just finished comparing the NEBNext Reagent...

I just finished comparing the NEBNext Reagent set 1 and Illumina’s paired end sample prep kit using different amounts of ChIP input DNA (1-10 ng). I used 2 different dilutions of Illumina’s PE...
Forum: Sample Prep / Library Generation 10-12-2010, 08:11 AM
Replies: 19
Views: 21,069
Posted By saikumarkv
Hi everyone, In a previous experiment I used...

Hi everyone,
In a previous experiment I used some MIRA enriched DNA (methylated) for a single read library prep (using Illumina Chip-seq kit) and sequencing, which worked very well. Right now I have...
Forum: Illumina/Solexa 10-07-2010, 11:42 AM
Replies: 16
Views: 8,663
Posted By saikumarkv
I talked to Kip @ Tufts sequencing core who is...

I talked to Kip @ Tufts sequencing core who is extremely helpful (thanks Kip) (http://genomics.med.tufts.edu/home/sampleprep), regarding their adapters. They now switched to phosphorothioate bond...
Forum: Introductions 09-18-2010, 11:36 AM
Replies: 373
Views: 143,940
Posted By saikumarkv
Hi everyone, This forum is awesome. We are...

Hi everyone,
This forum is awesome. We are just beginning to provide Illumina sequencing services as part of our Genomics Sequencing and Microarray Core at Cincinnati.
sai
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