This NSF-funded project is a collaborative effort between the Goldberg laboratory at UCLA and the Harada laboratory at UCD to understand what are all the genes required to make a soybean seed. We used soybean and Arabidopsis Affymetrix GeneChips, Laser Capture Microdissection (LCM), and next-generation high-throughput sequencing technologies to profile the mRNA sets present in different seed regions and compartments throughout development. Our long-term goal is to understand the genes and regulatory networks required to make a seed. Click here to learn more about this project and what has been accomplished.
To date, we have profiled the mRNA sets present in 71 soybean and Arabidopsis seed compartments from preglobular- to early maturation-stage seeds. All GeneChip data are stored in this web-based database. Under the Soybean GeneChip Experiments and Arabidopsis GeneChip Experiments sections on top, we created the built-in analysis tools to allow the user to not only browse the database by probe identification, gene ontology, and functional category, but also compare gene activity in different seed compartments during development.
Besides GeneChip experiments, we used next-generation high-throughput sequencing technology to profile soybean whole seed mRNAs from five developmental stages, 40 seed region and sub-region mRNAs captured by LCM, and seed cotyledon mRNAs from maturation through germination. To learn more and access the datasets along with user-friendly Excel data summary files, choose the experiment: RNA-Seq and GeneChip.
To understand what other factors, such as epigenetic events and small RNAs, may contribute to soybean seed development, we characterized DNA methylation changes during soybean seed development and small RNA profiles in 40 different seed region and sub-regions during soybean seed development. All datasets are submitted to NCBI Gene Expression Omnibus. We included all datasets with GEO links under Datasets & Resources section on top. Click the text below to access other resources that we provided for the soybean community:
Professor Goldberg created and currently teaches a novel course series that is a part of this NSF-sponsored project. The course series contains a lecture course, HC70A - Genetic Engineering in Medicine, Agriculture, and Law and a lab course, HC70AL - Gene Discovery Lab. This novel course series targets non-science majors and entering life science students. Professor Goldberg's objective is to teach undergraduates about the excitement of discovery, the process by which science is carried out, how advances in biology affect our daily lives, and how science is taught. Professor Goldberg and Professor Harada also used long-distance learning to teach students simultaneously at UCLA, UC Davis and Tuskegee University. Click here to learn more details about this unique teaching program.