venanciogroup

venanciogroup provides an RNA-seq expression atlas for soybean (Glycine max) built from 1,298 publicly available RNA-seq samples covering diverse tissues, developmental stages, and genotypes.

Key Features:

• Systematic Data Collection: Aggregates 1,298 publicly available RNA-seq samples from diverse tissues, developmental stages, and genotypes of soybean (Glycine max).
• Data Processing and Mapping: Processes raw sequencing reads and maps them to the soybean reference genome.
• Gene Expression Insights: Detects expression for 52,737 of 56,044 annotated genes (94%) in at least one sample.
• Clustering Analysis: Unsupervised clustering identifies three major groups corresponding to aerial, underground, and seed/seed-related tissues.
• Housekeeping Genes Identification: Identifies 452 genes with uniform and constant expression across samples as candidate housekeeping genes.
• Tissue-Biased Expression: Reports 1,349 genes with heavily biased expression toward specific tissues.
• Transcript-Level Analysis: Finds that 70,963 of 74,490 known transcripts (95%) overlap with those in the dataset and detects 3,256 potentially novel splicing isoforms.

Scientific Applications:

• Genetic and Genomic Research: Serves as a resource for soybean genetics and genomics studies on gene function, regulation, and evolution.
• Functional Genomics: Enables investigation of gene expression dynamics across tissues and developmental stages to aid functional annotation.
• Breeding Programs: Informs breeding strategies by providing data on tissue-specific and housekeeping genes relevant to yield, stress resistance, and nutritional content.

Methodology:

Collected 1,298 public RNA-seq samples, processed raw sequencing reads, and mapped reads to the soybean (Glycine max) reference genome.