Zea mays B73 seedling primary and seminal root tips (0-1mm), RNA-seq, steady-state transcription data

Zea mays B73 seedlings were grown for 3 days at 28C under low level fluorescent lighting. Terminal 0-1 mm root segments from primary roots only, seminal roots only, and primary + seminal roots combined were excised on ice and snap frozen. The tissue was ground with mortar and pestle in liquid nitrogen and RNA was extracted using the Invitrogen Plant RNA Purification Reagent. DNA was removed using the Invitrogen Turbo DNA Free kit. Ribosomal RNA was depleted using the Vazyme Ribo-off rRNA depletion kit for plants. RNA-seq libraries were made using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina in combination with NEBNext Multiplex Oligos for Illumina, Unique Dual Index UMI Adaptors RNA Set 1. For library preparation, an input of 25 ng of RNA was used for each sample; the protocol to target 200 nt inserts was followed; random primers for first strand cDNA synthesis were used; and the adapter ligated libraries were amplified for 9 PCR cycles. The average library size (insert + 150 bp adapter) ranged from 315-336 bp making the average insert size 165-186 bp. Libraries were sequenced using 150 bp PE on one lane of the NovaSeq 6000 S4 flow cell, using custom i7 cycles of 19 cycles to pick up the i7 index (8 nt) plus the 11 nt UMI. The UMI sequences have been appended to the read headers in the R1 and R2 files during demux with BCL Convert and after read alignment can be used by software, such as UMItools, to identify PCR duplicate reads.