RNA-seq Analysis of PpBURP-OE1 Plants

Three biological replicates (3 plants each) of wild-type (WT) and PpBURP-OE1 plants were sampled for RNA sequencing. The total RNA was extracted using the TRIZol™ Reagent (Life Technologies). RNA-seq library was constructed with the TruSeq RNA Sample Preparation v2 Guide (Illumina), and RNA sequencing was conducted with Illumina Hiseq 2,500 at Shanghai Personal Biotechnology Co., Ltd. (Shanghai, China). After filtering adapters and low-quality reads, the paired-end reads were then aligned to the reference genome of rice using HISAT2 v2.1.0 (Kim et al., 2019 (link)). Fragments per kilobase per million mapped (FPKM) reads was then calculated to estimate the expression level of the genes. Analysis of Gene Ontology (GO)⁷ enrichment was implemented by GOseq in R/Bioconductor packages based on the Wallenius non-central hypergeometric distribution (Young et al., 2010 (link)).

Free full text: Click here

Yu S., Yang F., Zou Y., Yang Y., Li T., Chen S., Wang Y., Xu K., Xia H, & Luo L. (2022). Overexpressing PpBURP2 in Rice Increases Plant Defense to Abiotic Stress and Bacterial Leaf Blight. Frontiers in Plant Science, 13, 812279.

Publication 2022

TRIZol™ Reagent TruSeq RNA Sample Preparation v2 Guide Hiseq 2,500

Biological Expression genes Genome Library Plants Rice Rna seq Trizol

Corresponding Organization :

Other organizations : Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences

Top 5 similar protocols

Variable analysis

independent variables

Wild-type (WT) and PpBURP-OE1 plants

dependent variables

Gene expression level (estimated by FPKM)

control variables

Total RNA extraction using TRIZol™ Reagent (Life Technologies)
RNA-seq library construction with TruSeq RNA Sample Preparation v2 Guide (Illumina)
RNA sequencing conducted with Illumina Hiseq 2,500 at Shanghai Personal Biotechnology Co., Ltd. (Shanghai, China)
Adapter and low-quality reads filtering
Paired-end reads alignment to the reference genome of rice using HISAT2 v2.1.0
Gene Ontology (GO) enrichment analysis implemented by GOseq in R/Bioconductor packages based on the Wallenius non-central hypergeometric distribution

Annotations

Based on most similar protocols

Etiam vel ipsum. Morbi facilisis vestibulum nisl. Praesent cursus laoreet felis. Integer adipiscing pretium orci. Nulla facilisi. Quisque posuere bibendum purus. Nulla quam mauris, cursus eget, convallis ac, molestie non, enim. Aliquam congue. Quisque sagittis nonummy sapien. Proin molestie sem vitae urna. Maecenas lorem.

As authors may omit details in methods from publication, our AI will look for missing critical information across the 5 most similar protocols.

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Revolutionizing how scientists
search and build protocols!