title: Dexamethasone treated mice   replicate 3
design: RNA was isolated from 20 day old tumor using Trizol and phenol:chloroform:isoamylalcahol extraction followed by ethanol precipitation. RNA quality control was using Bioanalyzer 2100 RNA 6000 NanoAssay chip (Agilent Technologies, Santa Clara, USA) and RNA above RIN = 8 was included for the study. The cDNA libraries were constructed by TruSeq RNA Library Prep Kit v2 (Illumina Inc., USA). Sequencing (100 bp paired end) was performed using Illumina Hi Seq2500 (Macrogen Inc. Korea). Imaging, base calling and quality scoring were done as per standard manufacturers guidelines (Illumina Inc., USA). The sequence quality was checked with FastQC,  adapter trimming was done with Trimmomatic. Reads were aligned with STAR aligner  against mouse reference genome {Genome Reference Consortium Mouse Build 38 (GCA_000001635.2)}. Transcriptome assembly and read counting were done using String Tie  and differential expression analysis was done using Ballgown.
library_name: HG_UD_DEX_R3