Total RNA was extracted from the roots of 21‐day‐old mock‐ and SA190‐colonized Arabidopsis grown on ½ MS with or without 25% PEG with the Nucleospin RNA plant kit (Macherey‐Nagel) following the manufacturer's recommendations. The quality and quantity of the RNA was assessed using Nanodrop‐6000 spectrophotometer, 2100‐Bioanalyzer (RNA integrity number greater than 8.0), and QubitTM 2.0 Fluorometer with the RNA BR assay kit (Invitrogen).
Nanodrop 6000 spectrophotometer
Manufactured by Thermo Fisher Scientific
The Nanodrop-6000 spectrophotometer is a laboratory instrument designed for the measurement of the concentration and purity of nucleic acids and proteins in small sample volumes. It utilizes a unique optical design that allows for the direct measurement of samples without the need for cuvettes or other sample holders. The Nanodrop-6000 provides accurate and reproducible results for a wide range of sample types and concentrations.
Automatically generated - may contain errors
2 protocols using nanodrop 6000 spectrophotometer
1
Arabidopsis Root RNA Extraction Protocol
2
RNA-seq Analysis of Arabidopsis Mutant
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RNA sequencing of 4-wk-old adult Col-0 and mta plants was performed with three biological replicates. RNA from mature leaves was extracted using Nucleospin RNA plant kit (Macherey-Nagel) following the manufacturer’s recommendations. The quality and quantity of the RNA was assessed using Nanodrop-6000 spectrophotometer, 2100-Bioanalyzer (RNA integrity number greater than 8.0), and QubitTM 2.0 Fluorometer with the RNA BR assay kit (Invitrogen). By using Illumina TruSeq standard mRNA Library Preparation protocol, RNA-seq was performed as per manufacturer’s instructions for 50 base pair paired-end sequencing. Pooled libraries were sequenced using Illumina HiSeq 4,000 platform. After trimming and read alignment, DESeq2 was run with read counts to identify DEGs between the genotypes with FDR ≤ 0.01 (Love et al. 2014 (link)). Functional enrichment of DEGs was carried out with AgriGO using default settings (Tian et al. 2017 (link)).
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