GSE60949
EWS-Fli and LNC regulated genes in comparison to GFP samples
RNA from A673 cells with shRNA-mediated knockdown of GFP (4 libraries),  EWS-FLI1 (4 libraries), or lnc277 (7 libraries) was isolated with TRIzol (Invitrogen).  Each sample was DNase treated and further purified on an RNeasy  Mini column (Qiagen) before quality analysis on an Agilent 2100 Bioanalyzer.  For each sample, 100-150ng of RNA was synthesized into cDNA, sheared on  a Covaris ultrasonicator, and amplified using the NuGen Encore Complete kit  (NuGen) to produce strand-specific and rRNA-depleted libraries. Samples were  multiplexed (4/lane) for 2x100bp paired-end sequencing on an Illumina HiSeq  2000 Overall design: RNA from A673 cells with shRNA-mediated knockdown of GFP (4 libraries), EWS-FLI1 (4 libraries), or lnc277 (7 libraries) was isolated with TRIzol (Invitrogen).