Do you think that there may be some non-random distribution of how RNA breaks in any sample determined by secondary structure? In other words, can you find any correlation between you bias that may be related on how RNA folds with itself?
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
@polivares: I have no idea. Seems like a possibility, but I'm not sure how to infer folding patterns, especially since we don't know how long the actual fragments are... only the first 25-30 bases or so... FYI: the fragmentation method was 'metal hydrolysis.'
Comment
-
So, it seems pretty clear to me now that the towers are caused by PCR. The Illumina protocol (http://grcf.jhmi.edu/hts/protocols/m...04898_RevA.pdf) fragments the mRNA, and then amplifies it by PCR. So if a breakage happens to occur at a particular location, the PCR amplified dataset would have several copies of the same fragment. Do I understand this correctly?
Also, if this is the problem, then this presents a bit of a problem for quantifying AS events. Is there a way to PCR the mRNA before fragmentation instead?Last edited by behoward; 09-23-2009, 07:19 AM.
Comment
Latest Articles
Collapse
-
by seqadmin
The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...-
Channel: Articles
05-06-2024, 07:48 AM -
-
by seqadmin
The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...-
Channel: Articles
04-22-2024, 07:01 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, Yesterday, 06:35 AM
|
0 responses
14 views
0 likes
|
Last Post
by seqadmin
Yesterday, 06:35 AM
|
||
Started by seqadmin, 05-09-2024, 02:46 PM
|
0 responses
19 views
0 likes
|
Last Post
by seqadmin
05-09-2024, 02:46 PM
|
||
Started by seqadmin, 05-07-2024, 06:57 AM
|
0 responses
18 views
0 likes
|
Last Post
by seqadmin
05-07-2024, 06:57 AM
|
||
Started by seqadmin, 05-06-2024, 07:17 AM
|
0 responses
19 views
0 likes
|
Last Post
by seqadmin
05-06-2024, 07:17 AM
|
Comment