title: Mock KD ES 3 RNA-Seq
design: RNA-Seq Expression
library_construction_protocol: mRNA was isolated from 3 ug total RNA using Dynabeads mRNA DIRECT   (Invitrogen) and fragmented with RNA fragmentation reagent (Ambion). First strand   cDNA synthesis was do ne with SuperScript III First-Strand Synthesis System and 3   ug/ul random hexamers (Invitrogen) followed by second strand synthesis with DNA   Polymerase I and RNase H. After purification, a sequencing library was generated from   the double stranded cDNA using paired-end adaptors (Illumina) and NEBNext DNA   Sample Prep Reagent Set 1 (NEB), and sequenced following a single-end sequencing   protocol. Sequencing was done on an Illumina Genome Analyzer GAIIX using Cluster   Generation v4 chemistry and Sequencing by Synthesis Kit v4. Data collection was   performed using Sequencing Control Software v2.6. Real-time Analysis (RTA) 1.6 was   used for data monitoring. Spliced mapping of RNA-Seq data was performed with TopHat   v1.0.14 using default parameters