Go Back   SEQanswers > Applications Forums > Sample Prep / Library Generation

Similar Threads
Thread Thread Starter Forum Replies Last Post
Removing bacterial contamination from plant tissue before sequencing serge73 Introductions 1 02-19-2018 05:50 AM
Extracting and classifying bacterial contamination from euakaryotic transcripts pig_raffles Bioinformatics 0 07-16-2015 08:14 AM
Bacterial contamination in salival sample ulz_peter Sample Prep / Library Generation 2 02-20-2012 11:57 AM
Contamination with bacterial rRNA JakobHedegaard Sample Prep / Library Generation 1 12-13-2011 08:48 AM

Thread Tools
Old 07-29-2020, 01:22 AM   #1
Senior Member
Location: Basel (Switzerland)

Join Date: Oct 2010
Posts: 208
Default Superscript IV bacterial contamination?

Dear all,
we have recently performed single-cell RNA-seq using a variety of methods and enzymes (Smart-seq2, Smart-seq3, Takara, etc). We observed that when using Superscript IV the number of reads "too short" to be aligned is sometimes 20-30% or higher...but we are using an oligodT to RT the mRNA. These too short reads turned out to align to bacterial rRNA (E.coli).
Many of the reagents are in common between protocols, so a contamination of other reagents is probably not the case here.

I remember that a few years ago there was a thread on this forum discussing the same issue for Superscript II and the conclusion was that some lots were contaminated (even if the company never admitted that). Did anybody have similar experiences lately?

Unfortunately we donīt have the lot number for many of the tubes we used but we are pretty sure that lot 00829693 (expiry date 2023/07/31) might be one of them.
Thanks for your help!
Simone78 is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 02:51 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO