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Bioinformatics

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