This project was initiated preceding the incorporation and standardization of KPIs. The progress of objectives are as follows:

Achieving objectives:
• As of the project end, most of the expected data was generated. The researchers had proposed to conduct bisulfite sequencing, small RNA, and mRNA analysis on materials which have undergone regeneration from tissue culture. These materials were to include two independent regenerated lines, at both the T0 (first transformed, or in this case, regenerated) line, and four generations later in the T4 generation. Plants from the same seed stock that did not undergo regeneration were to be analyzed as controls. They were able to complete data generation from 10 libraries.
• Replicated library sets were sequenced and the final total coverage of the libraries was ~30X (or 15X per strand of DNA, ideal for the identification of differentially methylated regions (DMRs).

Not Achieving the objectives:
• While this project has ended, not all the final steps are completed. Data analysis is still underway. This will involve (1) the identification of DMRs from the BS-seq data, the comparison of the DMRs with the small RNA data, using the small RNAs as validation of the DMRs (since they usually correlate very well), and the identification of any differentially expressed genes in the mRNA data that may result from the DMRs triggered by the tissue culture.
• The researchers anticipate that the DMRs will be characterized by the end of 2014, and the integration of small RNA and mRNA will follow as will publications of the results.