Some Large Diversity RNA-seq Data Sets
By Jinliang Yang, , 0

Some large scale RNA-seq data sets for diverse lines.

1. Shoot Apical Meristem (SAM) RNA-seq data from Leiboff et al., 2015

Data summary:

  • Study description: to study the genetic networks regulating structure and function of the maize shoot apical meristem
  • SRA Study ID: SRP055871
  • Sample Size: 369 maize inbred lines
  • Data Size: 2.7 Tbp; and 1.7Tb in size
  • Tissue: SAM-enriched apices of 14-day-old seedlings
  • Platform: HiSeq2000
  • Phenotype: Some SAM phenotypes Leiboff et al., 2015

2. Expression data of 368 lines from Li et al., 2013 and Fu et al., 2013

Data summary:

  • Study description: We explored the gene expression profiles of developing maize kernel by RNA sequencing. Our purpose was to explore the sequence diversity across the inbred lines, especially in the gene regions, and to discover the gene regulatory networks employed in immature maize kernels.
  • SRA Study ID: SRP026161
  • Sample Size: 368 maize inbred lines
  • Data Size: 2.4 Tbp; and 1.3Tb in size
  • Tissue: immature seeds after 15 DAP
  • Platform: with 200-bp insert size, 90-bp paired-end Illumina sequencing
  • Phenotype: oil-related traits from Li et al., 2013

3. Maize Pan-Transcriptome from Hirsch et al., 2013

Data summary:

  • Study description: Transcriptome or Gene expression.
  • SRA Study ID: SRP018753
  • Sample Size: 503 maize inbred lines (465 lines from the Wisconsin Diversity Set)
  • Data Size: 1.2 Tbp; and 0.8Tb in size
  • Tissue: Whole-seedling tissue including roots at the V1 stage from three inbred line was pooled.
  • Platform: Illumina HiSeq at the JGI to generate 100 nucleotide paired-end reads
  • Phenotype: some leaf traits and flowering time traits from Hirsch et al., 2013