RNA-seq datasets with GxE
By Emily Josephs, , 0

Some datasets with information about genetic differences for expression response to various stimuli (some stressful perhaps).

1. Natural variation for gene expression responses to abiotic stress in maize from Waters et al., 2016 and Transposable Elements Contribute to Activation of Maize Genes in Response to Abiotic Stress from Makarevitch et al. 2015

Data summary:

  • Study description: Measuring expression response to heat and cold conditions in inbreds and F1 hybrids and expression response to UV and salt in inbreds. They also look at relationships between TE presence and expression.
  • SRA Project ID: PRJNA244661 Note that this project only has data from the inbred lines, not F1s.
  • Sample Size: 5 inbred lines (B73, Mo17, Oh43, B37, and PH207) and F1 hybrids (B73xOH43, B73xMo17, B73xPH207). 3 biological reps per seedling
  • Data Size: 85 GB
  • Processed data: Gene and allele-specific expression counts for all samples are available in Dataset S1 from Waters et al., 2016
  • Tissue: 14 day old seedlings
  • Treatment: Cold = 7C for 16 hours. Heat = 50C for 4 hours. Control = 24C with 16 hour days. UV = , Salt =
  • Platform: Illumina HiSeq-2000

2. Transcriptome sequencing reveals the roles of transcription factors in modulating genotype by nitrogen interaction in maize from Chen et. al

Data summary:

  • Study description: Measuring expression in normal and low nitrogen conditions in two inbred lines to identify GxE (or GxN they call it) genes.
  • SRA Project ID: PRJNA272651
  • Sample Size: 4 line x treatment combinations, one rep each in SRA. The paper implies that there are two reps per combo however, so this is confusing.
  • Processed data: Info about GxN genes in a word document table here
  • Tissue: Leaf above primary ear
  • Treatment: Normal nitrogen has 450 kg/ha of urea and low nitrogen has no fertilizer.
  • Platform: Illumina HiSeq-2000