Transcriptome data of rice roots after applying NH1 strain under cadmium stress
Description
Transcriptome data of rice roots after applying NH1 strain under cadmium stress
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The present study selected rice root samples from four treatment groups (CK, NH1, Cd, and Cd+NH1) for transcriptome analysis, with six biological replicates per treatment, totaling 24 samples. Sequencing services were performed by Magigene Biotechnology Co., Ltd. (Guangdong, China; https://www.magigene.com/). Detailed experimental procedures and data analysis workflows are outlined below：Total RNA was isolated from each sample. After quality verification, mRNA was enriched using magnetic beads with Oligo(dT). The mRNA was fragmented using fragmentation buffer and reverse-transcribed into first-strand cDNA using random hexamer primers. Second-strand cDNA synthesis was subsequently performed using buffer, dNTPs, DNA polymerase I, and RNase H. Double-stranded cDNA was purified with AMPure XP beads, followed by end repair, poly-A tailing, and adapter ligation. Target fragments were size-selected using AMPure XP beads, amplified via PCR, and purified to generate sequencing libraries.Qualified libraries were sequenced on the Illumina NovaSeq platform with paired-end 150 bp (PE150) reads. Raw reads generated through base calling were subjected to quality control using fastp software to remove low-quality sequences. Ribosomal RNA sequences were filtered by aligning processed data to reference sequences from the NCBI RefSeq and Rfam databases using Bowtie 2 software, yielding high-confidence clean reads for downstream analyses. Clean reads were assembled into transcripts using StringTie. Transcript-level quantification was performed with Salmon software to obtain read counts. These counts were subsequently converted to gene-level read counts via the tximport package in R, thereby establishing the foundation for differential gene expression analysis.
Institutions
- Shandong Agricultural University