Hi, I have a RNA sample from Trizol RNA extraction with Bioanalyzer QC 28s/18s:1.8 and RIN 9.4. However, there is a high peak below 200nt. Can I use this sample for RNA-seq? Pls also see the attached RNA profile
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
Originally posted by Ken_HK View PostHi, I have a RNA sample from Trizol RNA extraction with Bioanalyzer QC 28s/18s:1.8 and RIN 9.4. However, there is a high peak below 200nt. Can I use this sample for RNA-seq? Pls also see the attached RNA profile
The only caveat I can think of is that if you are doing standard RNAseq, input amounts of RNA may not be calibrated for large percentages of the total RNA prep being small RNAs. It should not present a problem in your case, but I have seen preps where it looked like >70% of the RNA was small.
If you are concern there are lots of methods to fractionate away the small RNAs. For example Zymo RNA clean up columns come with a method for washing off small RNA prior to eluting.
--
Phillip
-
Thx for your answer. But do you think is there any chance that those peaks are DNA fragments? Moreover, I used the RNA 6000 pico kit. Will that be more sensitive to small fragments compare with nano kit and that's why I have a high cluster of peaks below 200nt?
Comment
-
Sure, they could be DNA fragments -- but to me this looks like a normal Trizol extracted RNA chromatogram. Overall pico chips are more sensitive than nano chips, obviously. But I have not noticed pico chips being unusually sensitive to shorter molecules.
Again, if the low molecular weight stuff is really bugging you, just get rid of it.
--
Phillip
Comment
-
I agree with pmiguel; this is typical of TRIzol extractions. Because I usually think DNAse treatment should remove all of the gDNA in the sample if used as directed, I won't worry much about gDNA contamination.
Of course pasing through a column would remove this peak, but this can also be done by isopropanol precipitation using a lower volume of isopropanol relative to the aqueous phase.
Comment
Latest Articles
Collapse
-
by seqadmin
The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...-
Channel: Articles
07-08-2024, 03:19 PM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 07-25-2024, 06:46 AM
|
0 responses
9 views
0 likes
|
Last Post
by seqadmin
07-25-2024, 06:46 AM
|
||
Started by seqadmin, 07-24-2024, 11:09 AM
|
0 responses
26 views
0 likes
|
Last Post
by seqadmin
07-24-2024, 11:09 AM
|
||
Started by seqadmin, 07-19-2024, 07:20 AM
|
0 responses
160 views
0 likes
|
Last Post
by seqadmin
07-19-2024, 07:20 AM
|
||
Started by seqadmin, 07-16-2024, 05:49 AM
|
0 responses
127 views
0 likes
|
Last Post
by seqadmin
07-16-2024, 05:49 AM
|
Comment