This NSF-funded project is a collaborative effort between Goldberg laboratory at UCLA and Harada laboratory at UCD to understand what the genes are required to make a soybean seed. We used soybean and Arabidopsis Affymetrix GeneChips, Laser Capture Microdissection (LCM), and 454 high-throughput sequencing technologies to profile the mRNA sets present in different seed regions and compartments throughout development. Our long-range goal is to understand the genes and regulatory networks required to make a seed. Click here to learn more about this project and what have been complished.
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 Soybean GeneChip and Arabidopsis GeneChip sections on the top, we created the built-in analysis tools to allow the user not only browse the database by probe identification, gene ontology, and function category, but also compare gene activity in different seed compartments during development. We also took efforts to annotate Affymetrix soybean array and Arabidopsis ATH1 array. To download the annotations and summaries, click here for Soybean Annotation and Arabidopsis Annotation.
The website also features a Genome Browser that integrates information for probe set annotation, the corresponding gene model, GeneChip expression data, and corresponding 454 ESTs, if available.
We also mapped individual probes to soybean predicted gene models (generated by the Department of Energy (DOE) Joint Genome Institute, Glyma version 1.01, released April 7, 2009) using BLASTN (≥ 23/25 nucleotide identity) to associate soybean array probe sets with soybean gene models. Click here to download the association of Soybean array probe sets and Soybean gene models under Annotation section.
Beside GeneChip experiments, we used 454 high-throughput sequencing technology to profile mRNA sets from soybean globular-stage seeds. Click here to learn more about it and download the raw 454 EST sequences under 454ESTs section.
Click here to see links related to this project.
