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.

一项针对乳腺癌原发肿瘤活检进行转录组学测量的临床研究，旨在分析不同时间点（相隔两周）采集的样本中二甲双胍对乳腺癌生物活性的影响。‘Poly (A) targeted’ mRNA 的下一代测序，包括文库制备，由牛津基因组学中心核心设施在惠康人类遗传学中心完成。本研究采用了新英格兰生物实验室的NEBNext mRNA Library Prep Master Mix Set进行表达文库的制备，并使用Illumina HiSeq 2000系统进行测序。配对读取数据通过Bowtie 2.2.6和Tophat v2.1与人类参考基因组GRCh38进行对齐，包括转录组信息。随后，利用Cuffdiff 2.2.1从对齐的读取数据中估算每个基因的标准化表达水平变化倍数，即FPKM（每千碱基转录片段数，每百万比对读取数）。