The database and the web pages that you see were produced by the Meyers lab at the University of Delaware. These 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.

Listed below are the different data sets that we have generated and the sites that we have developed for accessing these data: Arabidopsis, Rice, Brachypodium, Medicago, Soybean, Maize, Gallus gallus (chicken), Magnaporthe, Grape.

Fauxlane is a peer proposal review system that allows students from participating institutions to exchange proposals. The target group of students are plant biology graduate students who are writing research proposals as part of a graduate course. Using Fauxlane gives those students the experience of a Federal review panel, including anonymous peer review and panel discussions; and the concept is modeled on NSF's proposal review system called "Fastlane". If you would like to use Fauxlane for your course, please contact Blake Meyers at the University of Delaware. This program was built on the OpenConf peer-review management software, with development supported by NSF Plant Genome Research Program award #0701745.

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:

Arabidopsis PARE Database

The site contains data from cleaved mRNAs, also known as “degradome” sequencing. 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 of miRNA-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.

Arabidopsis Small RNA Database

The site contains data from an extensive collection of SBS-based small RNA libraries (ours and from Genbank). This data set was generated under NSF, USDA and DOE funding.

Arabidopsis DNA Methylation Database

The site contains BS-seq data from a collection of libraries including those from our lab, our collaborators and some from Genbank. This data set was generated under NSF funding.

Arabidopsis MPSS Plus Database

NOTE THAT THE DATA IN THIS DATABASE ARE FROM AN OBSOLETE TECHNOLOGY; The site contains MPSS mRNA tags (DpnII) and MPSS/454 small RNA data. This is our original website, and is now old data (but still useful in many cases). This older data are inferior to Illumina's SBS-based data. 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), and a "Small Grant for Exploratory Research" (SGER). The mRNA data includes at least 17 Arabidopsis MPSS libraries that comprise more than 43 million total signatures. There are also 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.

Our rice databases are organized to reflect the varied type of next-gen-based data that is now being generated. A quick overview of our organization:

Rice PARE Database

The site contains data from cleaved mRNAs, also known as “degradome” sequencing. The PARE data set, named for the "Parallel Analysis of RNA Ends (PARE)", includes libraries of 20-nt mRNA fragments publicly available from GEO at NCBI. 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 of miRNA-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.

Rice Small RNA Database

The site contains data from an extensive collection of SBS-based small RNA libraries. The small RNA SBS data includes public libraries available from GEO at NCBI.

Rice Small RNA Database 2

The site also contains data from an extensive collection of SBS-based small RNA libraries, but non-overlapping with the data in the site above. The site represents the full-dataset from a recent publication described on the main page of this site.

Rice ChIP Database

The site contains ChIP-seq data for rice generated either by our lab, collaborators, or public datasets from Genbank and other sources.

Rice DGE Database

The site contains data generated via a restriction-enzyme anchored tag from the 3' end of the transcript; SBS based data from cDNA cut with DpnII. The tag-based mRNA SBS data on this site includes a large set published in Genome Research that are also available from GEO at NCBI.

Rice DNA Methylation Database

The site contains BS-seq data from a collection of libraries including those from our lab and from Genbank. This data set was generated under NSF and USDA funding.

Oryza glaberrima RNA-seq Database

This site contains data from the African cultivated rice species, with the transcriptional data generated by our lab, built on a genome assembled by the OMAP project.

Oryza glaberrima Small RNA Database

This site contains data from the African cultivated rice species, with the transcriptional data generated by our lab, built on a genome assembled by the OMAP project.

Rice MPSS Database

NOTE THAT THE DATA IN THIS DATABASE ARE FROM AN OBSOLETE TECHNOLOGY; the older data are inferior to Illumina's SBS-based data. The 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.

Indica Rice MPSS Database

NOTE THAT THE DATA IN THIS DATABASE ARE FROM AN OBSOLETE TECHNOLOGY; We have developed a set of indica (variety: 93-11) mRNA MPSS data based on the Beijing Genome Institute whole-genome shotgun draft sequence and aligned by TIGR against the japonica (Nipponbare) sequence.

This data set was generated primarily with support from USDE's Plant Feedstock Genomics for Bioenergy Program (award #DE-FG02-07ER64450). The project is a collaboration between the University of Delaware laboratories of Pam Green and Blake Meyers. At the current time, we are working on generating the Brachypodium small RNA, PARE and mRNA libraries.

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.

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.

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

Maize Small RNA WGS Database

The site contains SBS small RNA data mapped to the complete genome. These small RNA data have been generated under NSF and USDA funding in the Meyers and Green labs, or have been collected from GenBank, or were generated in collaboration and with 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 the complete genome from the maize genome sequencing project.

Maize Small RNA 149 Database

The site contains SBS small RNA data mapped to several contigs on chromosomes 1, 4 and 9. These small RNA data have been generated under NSF and USDA funding in the Meyers and Green labs, or have been collected from GenBank, or were generated in collaboration and with 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.

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.

NOTE THAT THE DATA IN THIS DATABASE ARE FROM AN OBSOLETE TECHNOLOGY; 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.

NOTE THAT THE DATA IN THIS DATABASE ARE FROM AN OBSOLETE TECHNOLOGY; 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.