Has anyone been using the TruSeq RNA Access kit? We have been getting a snoRNA (SNORA63) soak up almost 10% of our reads from libraries we've generated with this kit. Seems to be present if we use high or low quality starting material. I'm attaching our Bioanalyzer traces, and you can clearly see there is an over-represented transcript present. I'm wondering if anyone else is having a similar issue? Any thoughts on whether this is due to insufficient post-capture washing? Thanks!
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
We have seen several different snoRNA's soak up reads in our analysis. We have been seeing the data improve recently by pre-heating the wash buffer during the second wash following captures. I can't say with absolute certainty that this will fix your problems. I think part of this problem begins with sample quality/complexity. Are you using FFPE material?
Comment
-
Unfortunately, I don't have any head to head comparison data to share. The snoRNAs are actually targeted by probes within the RNA Access oligo pool, so in many cases there is nothing you can do do get rid of them. We implemented the heated wash step because we figured it couldn't hurt. The workflow generates such high exonic mapping rates that we simply stopped worrying about the contaminating snoRNAs. At the end of the day, their presence wasn't dramatically affecting our work.
What alignment rates are you seeing for snoRNA's in your experiment?
Comment
Latest Articles
Collapse
-
by seqadmin
Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...-
Channel: Articles
03-22-2024, 06:39 AM -
-
by seqadmin
The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.
Avian Conservation
Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...-
Channel: Articles
03-08-2024, 10:41 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, Yesterday, 06:37 PM
|
0 responses
10 views
0 likes
|
Last Post
by seqadmin
Yesterday, 06:37 PM
|
||
Started by seqadmin, Yesterday, 06:07 PM
|
0 responses
9 views
0 likes
|
Last Post
by seqadmin
Yesterday, 06:07 PM
|
||
Started by seqadmin, 03-22-2024, 10:03 AM
|
0 responses
49 views
0 likes
|
Last Post
by seqadmin
03-22-2024, 10:03 AM
|
||
Started by seqadmin, 03-21-2024, 07:32 AM
|
0 responses
67 views
0 likes
|
Last Post
by seqadmin
03-21-2024, 07:32 AM
|
Comment