Supplementary data associated with two publications contrasting gene expression during somatic and zygotic embryo development and identifying long intergenic non coding RNAs during somatic embryogenesis

RNA-Seq data was generated from stages of somatic (SE) and zygotic embryogenesis (ZE). The developing zygotes (Zem) were isolated from the female megagametyophyte (FG) tissue at later stages. Differential expression analysis was performed for each dataset and the results were compared to identify common and contrasting expression changes. The somatic embryogenesis data was used to predict long intergenic RNAs and a co-expression network was generated. The network was used to assign putative functional annotation to the lincRNAs using a guilt-by-association approach. The normalised expression values, results of differential expression test, results of functional enrichment of gene sets and figures representing these are included. The sequences of identified lncRNAs are included as well as annotation information. The data is structured in three folders: SE = Somatic Embryogenesis ZE = Zygotic Embryogenesis SE_ZE = All files related to the comparison of differentially expressed genes between the two datasets. Some of the file names or figures can contain abbreviations different from the ones in the original publications. A conversion table is provided in the README file. More information on the folder and file content can be found in the manifest file.