These data have been generated by a series of different projects, mainly based at the University of Delaware and funded primarily by grants from the National Science Foundation and the United States Department of Agriculture. The database and the web pages that you see were produced by the Meyers lab, with data generated within our lab, by collaborating laboratories like the Green or Wang labs. Some data we've gathered from Genbank or other public sources. Much of the data was produced under contract by Illumina, Inc (Hayward, California), but some SBS libraries are now being sequenced at other sites.

The data are freely available, but we ask that you cite this web page or related publications; most libraries have been published as part of specific papers, but the best general citation for the website is Nakano et al. (2006) NAR 34(Database issue):D731-5. We would also like to know that you have found our data to be useful, so please let us know if you use data from this page. Please note, however, that the availability of this data and information does not constitute scientific publication; we request that you respect our right to publish on the complete data sets.

These data may contain errors or be incomplete, and should only be considered as a starting point for additional studies, or for comparisons. We do use some formulas for calculation of normalized values that can result in changes in these values as new libraries are added, although these changes will normally be quite small (e.g. not significant).

Listed below are the different data sets that we have generated and the sites that we have developed for accessing these data.

We have re-organized our Arabidopsis databases to reflect the varied type of short-read data that is now being generated. A quick overview of our organization:

The PARE site contains:
SBS mRNA tag data (DpnII) and PARE tags
Note that while we are working on DpnII tag data, the current dataset is all MPSS-based (old data)

The SBS site contains:
SBS mRNA tag data (NlaIII) and SBS small RNA data
Note that we have no NlaIII data, so no mRNA tags are shown for now.

The MPSS Plus site contains: MPSS mRNA tags (DpnII) and MPSS/454 small RNA data
Note that this is our original website, and is now old data (but still useful in many cases)

Arabidopsis PARE Database

The PARE data set, named for the "Parallel Analysis of RNA Ends (PARE)", was generated with DOE, NSF and USDA funds, and includes libraries of 20-nt mRNAfragments. The method represents a modified 5'-Rapid Amplification of cDNA Ends (RACE) reaction, combined with high-throughput deep sequencing (SBS) to create libraries that contain 3' cleavage products of mRNAs. Products ofmiRNA-directed cleavage are a result of "Slicer" (ARGONAUTE) activity which leaves a ligation-competent mRNA end with a 5' phosphate. In contrast, most mRNAs will be ligation incompetent during library preparation due to the 5'cap or because they lack a 5' phosphate. Many of the sequences that appear in PARE libraries are the products of mRNA decay and are not miRNA-directed cleavage products, and those data are also useful for examining gene expression and decay. The Arabidopsis PARE data are available if you select this link or click on the button below.

Arabidopsis SBS Database

The mRNA SBS data has yet to be generated/released. The small RNA SBS data on this site was generated under NSF, USDA and DOE funding. The Arabidopsis data are available if you select this link or click on the button below.

Arabidopsis MPSS Plus Database

The mRNA data set was the first generated by this project under NSF funding, including grants from these programs: Plant Genome Research, Genes and Genome Systems (MCB), Small Grant for Exploratory Research. The mRNA data includes at least 17 Arabidopsis MPSS libraries that comprise more than 43 million total signatures. More recently, we added small RNA data, based on MPSS and 454; the techniques for the parallel sequencing of small RNAs were developed with Pam Green's lab, also here at the University of Delaware. The Arabidopsis data are available if you select this link or click on the button below.

These mRNA and small RNA data have been generated under NSF and USDA funding. This includes grants from NSF's Plant Genome Research Program, and the USDA Plant Genome Program. This project is a collaboration with the laboratory of Guo-liang Wang at Ohio State, as well as with Pam Green's lab here at the University of Delaware. Our next phase of web site development will include the release of small RNA data based on Illumina's SBS method. The rice data available if you select this link or click on the button below.

This data set was generated primarily with support from USDA's Plant Genome Program (CSREES award #2006-03567). The project is a collaboration between the University of Delaware laboratories of Janine Sherrier, Pam Green, and Blake Meyers. At the current time, we are working on generating the Medicago small RNA libraries, with no plans to offer mRNA data (due to the nature of our grant). These data will be available if you select this link or click on the button below.

These small RNA data have been generated under NSF and USDA funding in the Meyers and Green labs, and NSF and NIH funding from Vicki Chandler's lab at the University of Arizona. This project is a collaboration between all three labs. The data include small RNA data based on SBS sequencing, and these sequences have been mapped to several high-quality contigs from the maize genome
sequencing project; the complete genome was not available at the time we built this database. The maize data available if you select this link or click on the button below.

This data set was generated primarily with support from USDA's Animal Genome Program (CSREES award #2007-35205-17947). The project is a collaboration between the University of Delaware laboratories of Joan Burnside, Robin Morgan, Pam Green, and Blake Meyers. At the current time, we are working on generating the chicken (Gallus gallus) small RNA libraries, with no plans to offer mRNA data. The small RNA data are available via this link or if you click on the button below.These data are available if you select this link or click on the button below.

This data set was generated partially under NSF award #0321437, and partially in collaboration with Illumina, Inc. These material was obtained from our collaborators in the laboratory of Guo-liang Wang at Ohio State. These data comprise two libraries from the fungal plant pathogen, Magnaporthe grisea, commonly known as rice blast. These data are available if you select this link or click on the button below.

This data set was also funded by NSF award #0110528 (Plant Genome Research Program), and it comprises one library from Cabernet Sauvignon, Stage II berries. The material was obtained from Dr. Alberto Iandolino at UC Davis. This library consists of more than 2.5 million signatures. At the time of our analysis, no grape genome was available, so the data were compared to ESTs to assign signatures to genes and to provide quantitative expression data for matching ESTs. These data are available if you select this link or click on the button below.