High-resolution expression profiling of selected gene sets during plant immune activation.
Pingtao DingBruno Pok Man NgouOliver J FurzerToshiyuki SakaiRam Krishna ShresthaDaniel MacLeanJonathan D G JonesPublished in: Plant biotechnology journal (2020)
The plant immune system involves detection of pathogens via both cell-surface and intracellular receptors. Both receptor classes can induce transcriptional reprogramming that elevates disease resistance. To assess differential gene expression during plant immunity, we developed and deployed quantitative sequence capture (CAP-I). We designed and synthesized biotinylated single-strand RNA bait libraries targeted to a subset of defense genes, and generated sequence capture data from 99 RNA-seq libraries. We built a data processing pipeline to quantify the RNA-CAP-I-seq data, and visualize differential gene expression. Sequence capture in combination with quantitative RNA-seq enabled cost-effective assessment of the expression profile of a specified subset of genes. Quantitative sequence capture is not limited to RNA-seq or any specific organism and can potentially be incorporated into automated platforms for high-throughput sequencing.
Keyphrases
- rna seq
- gene expression
- single cell
- high resolution
- genome wide
- genome wide identification
- dna methylation
- electronic health record
- big data
- cell surface
- high throughput sequencing
- transcription factor
- mass spectrometry
- machine learning
- cell wall
- deep learning
- bioinformatics analysis
- cancer therapy
- data analysis
- oxidative stress
- gram negative
- heat stress
- real time pcr
- nucleic acid