Friday, May 13, 2011

Visit Epicentre at the ASM 2011 General Meeting

Epicentre will be at the 111th American Society for Microbiology General Meeting, March 22-24, 2011, at the New Orleans Convention Center. Stop by booth 1737 to learn about our novel Nextera™ library preparation products for next-generation sequencing, ScriptSeq mRNA-Seq library preparation products, and Ribo-Zero™ rRNA removal kits.

We’ll be available to guide you through the best solutions for your research, including our broad assortment of kits for nucleic acid purification, PCR, genomic library production, and the EZ-Tn5™ Transposon tools. Exhibit hours are Sunday and Monday, May 22 and 23 from 10:30 a.m. through 4 p.m., and Tuesday, May 24, from 10:30 a.m. through 2:30 p.m.

We look forward to meeting you at the conference!

Tuesday, May 10, 2011

Ribo-Zero rRNA removal from FFPE RNA

One of the key benefits of the Ribo-Zero™ family of rRNA removal products is their ability to remove rRNA from partially degraded total RNA samples. We recently presented data on the performance of Ribo-Zero Kits with formalin-fixed, paraffin-embedded (FFPE) samples at the AACR 2011 Annual Meeting.

RNA from FFPE breast tumor tissue was used as starting material to prepare a mRNA-Seq library. The RNA sample was treated with the Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat) prior to library preparation using the ScriptSeq™ mRNA-Seq Library Preparation Kit (Illumina®-Compatible). Single-lane, 54-nt unidirectional sequencing reads were obtained using an Illumina® GAII sequencer, and sequence alignment was performed by Beijing Genomics Institute (BGI) with both the well-annotated human genome (ENSEMBL56) and in-house built junction sequences using BWA software allowing for four mismatches. The results were compared to those obtained from a library prepared without Ribo-Zero treatment.

(click to enlarge figure)

The Ribo-Zero-treated sample contained 76% of all 49,222 possible expressed genes with 0.24% of the reads being rRNA, compared to 48.8% rRNA reads for the untreated samples. As seen in the figure, Ribo-Zero treatment significantly increases mapped reads for exon, intergenic, and intron transcripts.