RNA-seq of Nipponbare: DHA-IAR embryo
RNA was extracted using the RNeasy Plant Mini kit (QIAGEN, Cat. No. 74904) according to the manufacturer's protocol. RNA integrity was assessed using the Agilent 2100 Bioanalyzer System.  Approximately 1 g of RNA was used for 3' mRNA-seq library preparation using the QuantSeq 3' mRNA-seq Library Prep Kit FWD (Lexogen). To minimize lane effects, samples were multiplexed using the Multiplexing Sample Preparation Oligo Kit (Illumina). Size selection was performed on a 2% agarose gel (Low Range Ultra Agarose, Biorad 161-3107). The denatured library was diluted to a final concentration of 6 pM and loaded into a flow cell (Illumina). After cluster generation, the multiplexed library was sequenced on an Illumina NextSeq 500 System (75 cycles, single-end, high output).