Deseq2: contains the scripts that we used for DGEA with deseq2 package in R.
Limma: contains the scripts that we used for DGEA with limma package in R.
Merging: contains scripts that we used for merging the mRNA data after DGEA with limma.

We used following GEO Datasets in total: miRNA: GSE43732: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43732 GSE6188: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6188 (discarded) GSE55857: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE55857 (discarded)

mRNA: GSE70409: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70409 GSE29001: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29001 GSE20347: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20347 GSE23400: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE23400