CTR Bioinformatics
The CTR offers a bioinformatics facility for members
Examples of the type bioinformatics support provided:
Experimental Design
- Replicates (biological vs technical)
- Sequencing choices (read length, depth etc)
RNA-Seq
- Differential gene expression
- Isoform expression
- Single cell sequencing (e.g. DROP-Seq)
Whole genome / Targetted sequencing
- Variant calling
Methylation Sequencing
- Whole genome / targetted sequencing
- Bisulfite (mC+hmC), oxidative bisulfite (mC), (h)MeDIP
- DMR calling
- Illumina 450K & EPIC array data analysis
RNA structure / RNA Interactions
- Prediction (2D and 3D)
- RNA motif discovery and searching
- RNA structure homology searching
Protein alignments / structure / interactions
- Multiple sequence alignments
- Homology modeling
- SILAC analysis
Microscopy Image Analysis
- Particle tracking
Training/Teaching
- Bespoke training (e.g. NGS Analysis, Introduction to Linux)
Teaching Materials
RNA-Seq for Differential Gene/Transcript Expression
| Presentation (PDF) | PlacentalBiologyCoursePresentation.pdf |
| Presentation (PPTX) | PlacentalBiologyCoursePresentation.pptx |
| R Code | PlacentalBiologyCourse_Sleuth.R |
| Link to publication | Stumpo et al (2016) Development |
| Samples | sample.descriptions_PlacentaVsYolkSac.txt |
Contact Russell Hamilton (rsh46@cam.ac.uk) for more details
