title: RNA-Seq of Mus musculus: aphidicolin + ATRi treated E14 cell line
design: RNA sequencing library was prepared using Rib0-Zero rRNA Removal Kit and TruSeq Stranded Total RNA library Prep kit. rRNA depleted RNAs were fragmented for 8 minutes at 94 ¡C. First strand and second strand cDNA were subsequently synthesized. The second strand of cDNA was marked by incorporating dUTP during the synthesis. cDNA fragments were adenylated at 3Õends, and indexed adapter was ligated to cDNA fragments. Libraries were multiplexed and clustered on 1 lane of flowcell. The samples were sequenced using a 2x150 Pair-End (PE) High Output configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS) on the HiSeq instrument. Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq program version 2.17. One mis-match was allowed for index sequence identification.