Experts in RNA-Seq

RNA-seq is a powerful, cost-effective tool of great interest in several life science areas. Thanks to high-throughput sequencing technologies this method is now available. RNA-seq allows us to obtain a large number of reads from the transcriptome. These reads are further analysed using high-throughput bioinformatic methods.

We sequence your species transcriptome

Today, RNA-seq is widely used by researchers in multiple life science areas. In the field of Comparative Genomics, scientists use RNA-seq to test whether the genes identified at the genomic level are also present in the transcriptome. In Biodiversity, RNA-seq is used to identify candidate molecular markers at any taxonomic level. In Molecular Ecology, this technology allows for an analysis of differentially expressed genes under given environmental stressors.

How we work

Our RNA-seq projects are divided into 4 steps. For your convenience, we can carry out the entire project or only the parts you need.

  • In Step 1 we isolate RNA either from flash-frozen samples or from samples preserved in an appropriate buffer (RNAlater® or equivalent).
  • In Step 2 we purify the RNA fraction you are interested in (total RNA, mRNA, small RNA) and construct a cDNA library.
  • In Step 3 we sequence the libraries using the Illumina HiSeq technology. Millions of reads per library are obtained in this step.
  • In Step 4 we carry out on-demand, high-throughput bioinformatic analyses in collaboration with ecSeq. The bioinformatic analyses provided are suited for a variety of RNA-seq experiments and goals, including:
    • Analysis of the transcriptome and its variability: de novo transcriptome assembly, gene and isoform prediction, gene quantification, differential expression analysis, and identification of non-standard RNA molecules (fusion-transcripts, circularised RNAs, etc).
    • Analysis of small ncRNAs: ncRNA prediction and quantification, differential expression analysis, microRNA target site prediction, custom ncRNA annotation, and RNA editing analysis.

Deliverables include your results, the raw data generated (which will be delivered through our server), and a summary of the methods followed.

RNA-seq data analysis with ecSeq

As new sequencing technologies continue to evolve, there is a growing need for bioinformatic expertise to handle, analyse, and interpret the exponentially-increasing amount of data generated. By partnering with ecSeq, a bioinformatic solution provider with solid experience in the analysis of RNA-seq data, we provide you with the latest advances in data analysis.

We will support you at each step of your project, from experimental design​ to data analysis. We are able to tailor our bioinformatic pipelines to your specific needs and can develop customised software tools. At the end of the project, you will receive a comprehensive methodological report containing the data analysis results, as well as the raw sequencing data.

By integrating the wet-lab and bioinformatic steps, our collaboration with ecSeq will help you to get the most out of your sequencing experiments, so that you can focus on answering your specific research questions.

Differential expression analysis in a microalgae

A research team from the Universidade da Coruña studied the effects of herbicide exposure on microalgae transcription. RNA from fresh cells from a number of treated and control cultures was extracted at AllGenetics. Then, we constructed cDNA libraries using the TruSeq RNA sample preparation kit. Libraries were pooled in equimolar amounts and sequenced in the HiSeq 2000 platform with the PE100 chemistry. The reads obtained were processed in collaboration with ecSeq. The results of this work unveiled upregulated transcripts related to heterotrophic energy generation.

Esperanza M, Seoane M, Rioboo C, Herrero C, Cid A (2015) Chlamydomonas reinhardtii cells adjust the metabolism to maintain viability in response to atrazine stress. Aquatic Toxicology 165:64-72.