miRNeasy kit (qiagen) used to extract Total RNA RNAomeSeq library preparation was performed using our own protocol. Total RNA was depleted of ribosomal RNA (RiboMinus, Life science) and subsequently fragmented (Covaris S200). Adapters were ligated to the fragmented rRNA depleted RNA pool (adapters from the TruSeq smallRNA kit v1.5) and cDNA was made by reverse transcriptase. After amplification of the cDNA (11 cycli) the RNA was fractionated to sizes of 15-500nt by gel. Indexes used for mRNASeq and RNAomeSeq (CGATGT: 8.3.3, TGACCA:  8.4.3, ACAGTG:  8.5.3,  GCCAAT: 8.4.16, CAGATC: 8.5.16, CTTGTA:  8.6.16) and smallRNASeq (CGATGT: 8.3.3, TGACCA:  8.4.3, ACAGTG:  8.5.3,  CGATGT: 8.4.16,  TGACCA: 8.5.16, ACAGTG:  8.6.16)
GEO Accession
GSM1167565