title: RNA-seq analysis of siFus-treated cells
design: Total RNAs were harvested from N2A cells in 6-cm dishes transfected with siRNA agianst Fus using RNeasy mini kit (Qiagen) according to the manufacture?s instruntion. 
library_construction_protocol: Briefly, the integrity and purity of total RNA were assessed using Agilent Bioanalyzer or Tapestation and OD260/280. 1-2 ?g of cDNA was generated from high quality total RNA using the Clontech SMARTer cDNA kit (Clontech Laboratories, Inc., Mountain View, CA USA, catalog# 634925). The resulting cDNA was fragmented using Covaris (Covaris, Inc., Woburn, MA USA) or Bioruptor (Diagenode, Inc., Denville, NJ USA), profiled using Agilent Bioanalyzer or Tapestation, and subjected to Illumina library preparation using NEBNext reagents (New England Biolabs, Ipswich, MA USA, catalog# E6040). The quality and quantity and the size distribution of the Illumina libraries were determined using an Agilent Bioanalyzer or Tapestation. The libraries were then submitted for Illumina HiSeq2000 or HiSeq2500 sequencing according to the standard operation. Paired-end 90 or 100 nucleotide (nt) reads were generated and checked for data quality using FASTQC (Babraham Institute, Cambridge, UK). If applicable, the data was then subjected to data analysis using the platform provided by DNAnexus (DNAnexus, Inc, Mountain View, CA USA) or the platform provided by Center for Biotechnology and Computational Biology (University of Maryland, College Park, MD USA) as previously described (Nature Protocols 7:562-578, 2012).