Centre for Trophoblast Research: Placental Bioinformatics Course

^{Version 0.3: 20180705}

Russell S. Hamilton (rsh46@cam.ac.uk), Xiaohui Zhao (xz289@cam.ac.uk) & Malwina Prater (mn367@cam.ac.uk)

An introduction to RNA-Seq

Objective for the practical

• To learn about how to process, analyse and interpret RNA-Seq data

Learning goals

• Experience using the Linux operating system (Ubuntu)
• Learn how to run bioinformatics tools on the command line
• Learn how to use R and R-studio
• Visualise sequencing alignments in a genome browser

Materials

Publication

The data are from

Stumpo, D.J., Trempus, C.S., Tucker, C.J., Huang, W., Li, L., Kluckman, K., Bortner, D.M. and Blackshear, P.J. (2016) Deficiency of the placenta and yolk sac specific tristetraprolin family member ZFP36L3 identifies likely mRNA targets and an unexpected link to placental iron metabolism. Development, 143, 1424-1433 doi:10.1242/dev.130369

And downloaded via EBI European Nucleotide Archive (ENA) from

• Yolk Sac
• Placenta

Presentation / Notes

• 2018_PlacentalBiologyCourse_Presentation.pdf
• 2018_PlacentalBiologyCourse_Presentation.pptx

Commands / Code

• 2018_PlacentalBiologyCourse_Commands.txt
• 2018_PlacentalBiologyCourse_Sleuth.Rmd

Reference Genome / Transcriptome

Gene to transcript table

• ENST_ENSG_GeneName.GRCm38.kallisto.table
• A Kallisto index for GRCm38 is required e.g. Mus_musculus.GRCm38.cdna.all.idx. See https://pachterlab.github.io/kallisto/starting.html for details how to create/download.

Sample Files with pre-made QC and alignments

• SRR1811706_ES610_WT_Yolk_Sac
• SRR1811707_ES611_WT_Yolk_Sac
• SRR1811708_ES612_WT_Yolk_Sac
• SRR1811709_ES613_WT_Yolk_Sac
• SRR1823638_ES51_WT_Placenta
• SRR1823639_ES51_WT_Placenta
• SRR1823640_ES52_WT_Placenta
• SRR1823641_ES52_WT_Placenta
• SRR1823642_ES53_WT_Placenta
• SRR1823643_ES54_WT_Placenta
• SRR1823644_ES55_WT_Placenta

Files Excluded from this distribution

A directory containing pre-made kallisto pseudoalignment files for samples SRR1823638_ES51_WT_Placenta and SRR1811706_ES610_WT_Yolk_Sac as they are too large to store here.

• IGV_Alignments/

License

Attribution-Non Commercial-Share Alike CC BY-NC-SA ( https://creativecommons.org/licenses/by-nc-sa/ )

	Attribution:	You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use.

	NonCommercial:	You may not use the material for commercial purposes.

	ShareAlike:	If you remix, transform, or build upon the material, you must distribute your contributions under the same license as the original.