Sean Stevenson - Gene expression analysis

Sean Stevenson

Gene expression analysis

Post Doctoral Researcher

University of Leeds

Description

I offer a high level of interaction and customisation for your next-gen sequencing analysis in comparison to the big sequencing companies.
• RNAseq pre-processing: Given your raw sequences (or a raw dataset on SRA database) I will carry out quality control and filtering to remove low quality and biased sequences.
Gene expression analysis: Given your pre-processed sequences, I will carry out gene expression analysis. This will include alignment or de novo assembly of transcripts depending on study organism and availability of reference genome. Transcript abundance used to quantify gene expression as function of control levels with tables of significantly up/down-regulated genes given alongside the raw data. Optional isomer level analysis (e.g. splicing variants) available if required.
• Post analysis: Further analysis including cluster analysis and cis-element enrichment available to understand co-regulation of genes of interest. Other possibilities can be discussed (e.g. metabolic pathway analysis).

I'm looking forward to working with you!

What do you need to provide us with?

The raw or pre-processed data depending on required stages. These will need to be compressed and data transfer instructions will be arranged. File formats can be in any as received from sequencing.

What will I deliver?

Gene expression data in the form of excel tables with raw (normalised and un-normalised) transcript abundance levels as well as significantly up/down-regulated genes for each treatment.
Gene cluster analysis with both images and the accompanying data as well as any cis-element analysis excel and text files.
Any other analysis can be discussed and arranged.

Publications


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Article: De novo assembly and comparative analysis of the Ceratodon purpureus transcriptome

Péter Szövényi, Pierre-François Perroud, Aikaterini Symeonidi, Sean Stevenson, Ralph S. Quatrano, Stefan A. Rensing, Andrew C. Cuming and Stuart F. McDaniel

Image representing an article
Image representing an article

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