Differential Expression of Dictyostelium discoideum RNAseq data

Identify Differential Expressed Genes in DgcA null mutant and Knock-out samples in Dictyostelium Discoideum. The same workflow has been used for the differential expression analysis of Polysphondylium pallidum.

Alterative Link

https://github.com/bartongroup/rs-Dictostelium_Differential_Expression_Experiment

Quality Control

R CMD BATCH QualityControl.R &

Alignmnet using Tophat

./try.sh

./try1.sh

./try2.sh

Alignmnet Visualization

R CMD BATCH InputIGV-HtseqCount.R

Read Count

R CMD BATCH htseq-count.R

Differential Gene Expression

R CMD BATCH DiffExpTwoGroup.R

Gene-Set Enrichment Analysis

R CMD BATCH GSEA.R

Publication

Chen ZH, Singh R, Cole C, Lawal HM, Schilde C, Febrer M, Barton GJ, Schaap P. Adenylate cyclase A acting on PKA mediates induction of stalk formation by cyclic diguanylate at the Dictyostelium organizer. Proceedings of the National Academy of Sciences. 2017 Jan 17;114(3):516-21.