Cotton Seed Development

Project description, data sheets and analytic scripts for transcriptomic and proteomic analsis of seed development in diploid and polyploid cotton species.

Paper 1

Hovav R, Faigenboim-Doron A, Kadmon N, Hu G, Zhang X, Gallagher JP, Wendel JF. 2015. A transcriptome profile for developing seed of polyploid cotton. The Plant Genome 8(1).

• data sheet - "RPKM values of cottonseed transcriptomes.txt"
• R script for clustering analysis and heatmaps - "clusteringAnalysis.txt"

Paper 2

Guanjing Hu, Ran Hovav, Corrinne E. Grover, Adi Faigenboim-Doron, Noa Kadmon, Justin T. Page, Joshua A. Udall and Jonathan F. Wendel. 2016. Evolutionary conservation and divergence of gene co-expression networks in Gossypium (cotton) seeds. Genome Biology and Evolution.

• data sheet - RNA-seq read count file - "All ADT not normalized.txt"
• data sheet - oil content and seed weight measuement - "oil_content073115.txt", "seed_weight.txt"
• R script for DESeq2 analysis - "deseq2.r"
• R script for differential coexpression analysis - "differentialCoexpression.r"
• R script for WGCNA network analysis - "Rcode_WGCNA_112315.r"
• Associated R source code- "multiplot.r", "multiscalefreeplot.r", "summarySE.r", "WGCNA_missingFun.r"