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-   -   More than half of Smart-seq2 data is TSO,ISPCR concatemers! (http://seqanswers.com/forums/showthread.php?t=90787)

Kujin Kwon 09-04-2019 06:00 PM

More than half of Smart-seq2 data is TSO,ISPCR concatemers!
 
Hi all,
Last month, I made fixed tissue (5< RIN < 7) RNA-seq library using SMART-seq2 method. (I thought single cell library prep method is suitable for fixed sample because of low quantity of RNA and even broken RNA could be captured by poly-A primer in RT )

However, I found that multiple TSO, ISPCR sequences were included in library reads(Mostly less than 300bp reads). Even though I checked library quality by DNA high sensitivity chip, but almost 50% of reads has mostly TSO oligomers.

Is there anyone who faced same problems? How can I solve this? Any suggestion would be welcomed

luc 09-05-2019 10:14 AM

What type of size selection did you use?
I guess, these results are likely due to the lack of size-selection and low inputs? since you were working low integrity/quality RNA samples from fixed tissues?

We have no experience with such samples, though.


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