Superscript IV bacterial contamination?

Simone78 · 07-29-2020, 01:22 AM

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 don´t 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!
Simone

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07-29-2020, 01:22 AM	#1
Simone78 Senior Member Location: Basel (Switzerland) Join Date: Oct 2010 Posts: 208	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 don´t 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! Simone