Name: A Comprehensive Transcriptomics Analysis Reveals Long Non-Coding RNA to Be Involved in the Key Metabolic Pathway in Response to Waterlogging Stress in Maize

Link to publication: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7140884/#B46-genes-11-00267

NCBI bioproject ID: PRJNA606824


Category: RNA-Seq, stress

Description:
Seeds of maize imbred line B73 were planted in a controlled environment  (~28 °C/22 °C day/light cycle), a 14 h/10 h light/dark cycle (light time: 7:00 am–9:00 pm), 
with an average humidity of 60%.  “Waterlogging” is described as flooding of the root system and “submergence” to describe the situation when most or all aerial tissue is under water. 
Ten uniform seedlings were planted in a plastic pot, and waterlog streses or treatments were applied by maintaining a 2–3 cm water layer above the substrate at the second leaf stage. 
Waterlogging stress was applied at time points 0h before treatment (control), and after treatment at 2 h, 4, h, 6 h, 8 h, 10 h and 12 h.

Total RNA was isolated from the roots tips of control and waterlogging stress treated maize plants using an TRIZOL reagent (Invitrogen, Gaithersburg, MD, USA) and purified with an RNeasy mini kit (QIAGEN, Germantown, MD, USA) 
following the manufacturer’s instructions.RNA-seq reads were mapped by MaizeGDB to Zm-B73-REFERENCE-NAM-5.0. using STAR. Bigwig files were generated using bedtools genomecov -split -scale 1.0 
followed by kentUtils bedGraphToBigWig.