RNASeq data from primary breast cancer clinical study pre- and post- two weeks treatment with metformin

A clinical study that measured transcriptomics from biopsies of primary breast cancer taken at paired time points two weeks apart to profile the bioactivity of metformin breast cancer. Next generation sequencing of ‘Poly (A) targeted’ mRNA, including library preparation, was carried out by the Oxford Genomics Centre core facility at the Welcome Trust Centre for Human Genetics. The NEBNext mRNA Library Prep Master Mix Set (New England Biolabs) was used for preparation of the expression libraries and the Illumina HiSeq 2000 system used to carry out the sequencing. Paired-read were aligned to human reference genome GRCh38, including transcriptomic information, by Bowtie 2.2.6 and Tophat v2.1. The fold change of normalized expression level, FPKM (Fragments Per Kilobase of transcript per Million mapped reads), for each gene was then estimated from those aligned reads using Cuffdiff 2.2.1.