ecotoxxplorer.github.io

RNAseq Analysis Tutorial

Minnow (ethinylestradiol) Dataset

This tutorial is prepared for the Minnow (ethinylestradiol) example dataset. In this experiment, Fathead minnows (FHM) were exposed to graded concentrations (Solvent, Low, Medium, and High) of ethinylestradiol (EE2, chemical 1) right after fertilization. Each treatment group has five replicates (A, B, C, D, E). After 7-days post fertilization (dpf), fish were sub-sampled for transcriptomic analyses. Only the Solvent, Medium, and High concentration treatments were used for sequencing. Therefore, a total of fifteen samples. The main objective of this specific study is to characterize molecular toxicity pathways of EE2 in FHM using transcriptomic analysis.

Tutorial Steps

1. Data Upload and Annotation
2. Data Summary and Quality Check
3. Data Filtering & Normalization
4. Differential Expression Analysis
5. Expression Tools for Interactive Analysis
   • Volcano Plot Tool
   • Heatmap Tool
   • Enrichment Network Tool
   • Pathway Dysregulation Analysis Tool