title: GSM3573744: Control rep 1; Oryza sativa Japonica Group; RNA-Seq
library_construction_protocol: Root systems were collected 3 days after nematode inoculation, which corresponds to 4 days after treatment with AO (20 U/mL). For each treatment, three independent biological replicates, containing a pool of 4-5 individual plants, were taken. RNA was extracted using the QIAGEN RNeasy Plant Mini kit according to the manufacturer's instructions, with additional sonication after adding extraction buffer RLT. RNA integrity was checked using the Agilent BioAnalyzer 2100 (Agilent). Approximately one microgram of total RNA was used for 3' mRNA-Seq library construction using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina. To minimize lane effects the samples were multiplexed, using the multiplexing sequencing adapters provided in the Multiplexing Sample Preparation Oligo Kit (Illumina). Size selection of the library 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 on a flow cell (Illumina). After cluster generation, the multiplexed library was sequenced on an Illumina NextSeq500 (75 cycles, single end, high output).