OHMX_High-throughput OMICS solutions
Transcriptomics
of FFPE
and other
low-quality
samples
Transcriptomics of FFPE
and other low-quality samples

Typically, RNA isolated from formalin-fixed, paraffin-embedded (FFPE) tissue is partially degraded and has a low overall quality.

We use the Lexogen QuantSeq 3′ mRNA-Seq Library Prep on FFPE samples. This is a cheap and ideal approach for genome wide analysis of gene expression studies, starting from total RNA as input material. The required input amount of total RNA is as low as 100pg. A high throughput version of the kit, with Illumina compatible dual indexing allows up to 9216 samples to be multiplexed in one lane.

Advantages of the Lexogen QuantSeq 3′ mRNA-Seq Library Prep

Affordable: only the 3′ part of each transcript is sequenced
Ideal for gene (mRNA) expression studies
High-quality data can be obtained from difficult / degraded samples
Sequencing is possible for low input amounts of RNA (0.1 ng)

Alternatively, we can use the Truseq Exome RNA kit for low quality samples. The kit provides a low-cost solution for analyzing (human) RNA. Starting from as little as 10 ng total RNA from intact samples or 20 ng total RNA from degraded samples, it is possible to achieve accurate, sensitive RNA-Seq results. Combining proven RNA library prep chemistry with efficient sequence-specific capture, the Truseq Exome RNA kit generates RNA-Seq libraries from degraded samples that focus on the RNA coding regions.

Advantages of the Truseq Exome RNA

Focusing on the (human) transcriptome coding regions

High-quality data can be obtained from difficult / degraded samples

Sequencing is possible for low input amounts of RNA (10 to 20 ng)

Workflow

The process starts by performing an initial quality check of the total RNA provided by you. During this quality check, the concentration and integrity of the RNA is determined. We only continue with samples that passed this initial quality check. If for some reason certain samples did not pass this initial check, we will contact you to discuss on how to proceed.

In the next steps, the RNA is captured (Illumina TruSeq RNA Access library prep kit) and transcribed (Illumina TruSeq RNA Access library prep kit / Lexogen QuantSeq 3′ mRNA-Seq Library Prep) to cDNA. From the cDNA, sequencing libraries are constructed, which are again quality checked.

Finally, the libraries are sequenced on one of our Illumina sequencers. The technical quality of the sequencing run is monitored in real time.

Raw sequencing data can be transferred to you via the ohmX.bio server (FTP download) or the Illumina BaseSpace platform.