We routinely provide assistance with the analysis of various NGS applications (RNAseq, ChIPseq, ATACseq to name a few) as well as single-cell RNAseq. We will also analyse data from microarray platforms such as gene expression arrays. In all cases we recommend that you come as see us so we can check your design, but also so that we are aware data will be forth-coming.
With advances in technology, new methods and techniques are constantly being developed, meaning that we also need to learn how to handle data coming from these new applications. If you are planning on generating any such data, please see us as soon as possible so we can prepare. This will reduce the waiting time between data production and getting results.
We also provide a computation platform hosted at Lunarc which is available to for those to use who have some experience of bioinformatics. Please see us and we will show you how to apply for access, and how to get started.
We can do the following:
- Microarray: pre-processing, normalisation, calculation of differentially expressed genes, and graphical outputs (heatmaps etc) - 17,000 SEK
- RNAseq: QC, mapping, quantification of transcripts, calculation of differentially expressed genes, and graphical outputs - 17,000 SEK
- ChIPseq/ATAC: QC, mapping, peak detection and annotation of peaks, production of wig files for visualisation - 17,000 SEK
- Single-cell RNAseq or ATACseq: QC, mapping, processing to UMAP/tSNE, identification of markers - 30,000 SEK. The analysis of single-cell data is often more complex depending on the question, so please see us before you do the experiment to see if we can take on your job.
- Spatial transcriptomics (10X Visium): 30,000 SEK
In all cases we will help to submit your data to GEO/ArrayExpress.
Any further analyses on your data will be performed time-permitting. Of course, if there are other uses of NGS which are not covered here please come and see us, and if you have any bioinformatics related issues/problems (such as reviewer comments) you are welcome to see us where we will help you as best as we can.
Book Our Services:
For bookings and consultations, please contact the facility manager: shamit [dot] soneji [at] med [dot] lu [dot] se (shamit[dot]soneji[at]med[dot]lu[dot]se)