Computational protocol: Basic leucine zipper transcription factor SlbZIP1 mediates salt and drought stress tolerance in tomato

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Protocol publication

[…] Eight-week-old WT and SlbZIP1-RNAi plants (mixed samples of six plants) were irrigated with water containing 400 mM NaCl from the bottoms of the pots, and then leaf samples were collected after 24 h. Then RNAs extracted from the salt-treated leaves were employed for the RNA sequencing using Illumina HiSeq 2500 platform, and the 150 bp paired-end reads were generated by Genepioneer Bioinformatics Institute (Nanjing, China). The clean reads were filtered from the raw reads by removing duplication sequences, adaptor sequences and low-quality reads. Cleaned reads were subsequently mapped to the tomato reference genome by HISAT2 software []. The quantitative information of the RNA-seq data can be seen in Additional file : Table S3. Gene expression abundance was analyzed using StringTie software [], to identify DEGs (differentially expressed genes), transcript abundance was normalized by FPKM (expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) method, and FDR (false discovery rate) ≤ 0.05 was used to determine the threshold for DEGs. Then qRT-PCR was carried out to validate the results of RNA-seq, and gene-specific primers used for qRT-PCR of selected stress-related genes were listed in Additional file : Table S2. […]

Pipeline specifications

Software tools HISAT2, StringTie
Application RNA-seq analysis
Organisms Solanum lycopersicum
Chemicals Chlorophyll