title: Entamoeba histolytica sequencing from TSS identification  experiment csRNA
design: Total RNA (10-100 g) was polyA enriched twice using Sera-Mag  Magnetic Particles Oligo(dT) coated (Thermo Scientific ref. 28152103011150)  and fragmented 5 minutes (Ambion ref. AM8740). According to manufacturer's  instructions, Transcription Start Site enrichment was achieved with  Terminator 5'-Phosphate-Dependant Exonuclease (TEBU ref. TER51020) followed  by Tobacco Acid Pyrophosphatase (TEBU ref. T81050) treatment. For CapSeq, total RNA was  similarly treated with an additional 15% TBE-urea gel size selection. RNA was treated with Terminator  5-phosphate-dependent Exonuclease (Epicenter ref. TER51020), calf intestinal  phosphatase (New England Biolab ref. M0290) and Tobacco Acid Pyrophosphatase (Epicenter ref. T19050). Libraries were constructed following manufacturer's  recommendations using TruSeq Small RNA Sample Prep Kit (Illumina, ref.  RS-200-0012). The libraries were purified with AMPure XP beads (Agencourt  ref. A63880) and controlled by Bioanalyzer DNA High Sensitivity Chips  (Agilent ref. 5065-4626). Sequencing has been performed on a HiSeq 2000  (Illumina) in a multiplexed 51+7 bases single read using a TruSeq SR Cluster  kit v2 cBot HS (Illumina, ref. GD-401-2510) and a TruSeq SBS kit v2 HS 50  cycles (Illumina, ref. FC-401-1002).