cDNA synthesis was performed using the SMARTer Ultra Low RNA kit for Illumina sequencing (Clontech) according to the manufacturer’s recommendations. cDNAs were synthesized, purified with Ampure XP beads and then amplified with 13 PCR cycles with Advantage 2 Polymerase Mix (50×, Clontech). The PCR products were purified on SPRI AMPure XP beads (Beckman Coulter), and the size distribution was checked on a high-sensitivity DNA chip (Agilent Bioanalyzer). cDNA libraries were prepared with TruSeq Nano DNA kit or Nextera XT DNA (Illumina). For TruSeq Nano libraries, 20–30 ng cDNA was sheared by sonication (parameters adjusted to obtain fragments from 350 to 450 bp). For Nextera libraries, 1 ng was fragmented by tagmentation. Then cDNA libraries were prepared according to the manufacturer’s recommendations. Samples were sequenced on an Illumina HiSeq 2000 at an average of 72.3 million 100-bp paired-end reads.