title: RNA-seq of A. thaliana: whole leaf mock infected 5dpi Rep 2
design: Plants were grown for 1 month in a growth chamber. At 1 month old, plants were mock innoculated with sap from N. benthamiana. After 5 days post innoculation, 2-4 of the youngest leaves were cut and flash frozen in liquid nitrogen. Leaves from ~18 plants were pooled together to form this sample. Samples were ground, lysed, and treated with proteinase K, DNase, Ribo-zero, and alkaline fragmented prior to size selection via gel extraction. Ends were repaired with T4 PNK enzyme and 3' and 5' 4N adenylated adapters were ligated on with the NEXTflex kit. Bead cleanup was performed after  adpater cleanup followed by cDNA amplification and gel size selection. Fragment sizes were verified on a Bioanalyzer, samples were pooled, then sequenced on a NovaSeq 6000 S1 flow cell for 100 cycles. Samples were split across both lanes of the flow cell to mitigate any potential lane bias. Reads from both lanes were combined into a single FASTQ file for each sample.