QIAseq FastSelect -5S/16S/23S Kit (96)

A bacterial rRNA removal solution from QIAGEN designed to enrich non-rRNA transcripts in downstream sequencing applications. Targeting 5S, 16S and 23S bacterial rRNAs, the kit addresses the challenge of metatranscriptomic studies, where conventional hybrid capture and species-specific enzymatic removal methods are inefficient against the diversity of the microbiome, including nearly 600,000 different 16S sequences and nearly 170,000 23S sequences.

The workflow accepts 20 ng to 1 µg of input RNA — including fresh, high-quality RNA, FFPE RNA or degraded samples — and integrates as a single step during reverse transcription with stranded RNA-seq library kits from QIAGEN, Illumina and NEB, such as the QIAseq Stranded Total RNA Lib Kit, TruSeq Stranded and NEBNext Ultra II Directional. Users add the reagent to the RNA sample, optionally perform fragmentation, stepwise cool the reaction from 75°C to 25°C over 14 minutes and carry out a bead-based cleanup before completing library preparation. Highly efficient rRNA removal is achieved in one hour, replacing alternative hybrid capture protocols that involve more than 25 steps and approximately 2 hours of pre-treatment.

In performance testing using total RNA isolated from Gut Microbiome Whole Cell Mix (ATCC), the kit removed over 90% of bacterial 5S/16S/23S rRNA compared to less than 10% removal achieved by alternative Supplier TF methods, freeing more than 85% of sequencing reads for gene expression analysis versus approximately 5% without rRNA removal. Unique genes detected (FPKM >0) increased 50%, from approximately 20,000 to over 30,000, with effective rRNA depletion observed across individual species including Bacteroides fragilis, Bacteroides vulgatus, Bifidobacterium adolescentis, Clostridioides difficile, Enterococcus faecalis, Lactobacillus plantarum, Enterobacter cloacae, Escherichia coli, Helicobacter pylori, Salmonella enterica and Yersinia enterocolitica. Store at -20°C and avoid repeated freeze–thaw cycles.