Project Support

The Arabidopsis Small RNA Project is supported generously by a 2010 Project grant from the National Science Foundation (MCB-0618433). The project uses facilities and resources provided by the Department of Botany and Plant Pathology, the Center for Genome Research and Biocomputing, Oregon State University.
NSF
Oregon State University
CGRB

Gustafson AM, Allen E, Givan S, Smith D, Carrington JC, Kasschau KD. (2005).
ASRP: The Arabidopsis Small RNA Project Database. Nucleic Acids Res 33, D637-40. Abstract

1. Kasschau, K.D., Fahlgren, N., Chapman, E.J., Sullivan, C.M., Cumbie, J.S., Givan, S.A. and Carrington, J.C. (2007) Genome-Wide Profiling and Analysis of Arabidopsis siRNAs. PLoS Biol, 5, e57. Abstract

2. Fahlgren, N., Howell, M.D., Kasschau, K.D., Chapman, E.J., Sullivan, C.M., Cumbie, J.S., Givan, S.A., Law, T.F., Grant, S.R., Dangl, J.L. et al. (2007) High-Throughput Sequencing of Arabidopsis microRNAs: Evidence for Frequent Birth and Death of MIRNA Genes. PLoS ONE, 2, e219. Abstract

3. Howell, M.D., Fahlgren, N., Chapman, E.J., Cumbie, J.S., Sullivan, C.M., Givan, S.A., Kasschau, K.D. and Carrington, J.C. (2007) Phasing Patterns and Genome-Wide Profiles of RDR6/DCL4-Dependent Small RNAs in Arabidopsis. The Plant Cell, 19, 926. Abstract

4. Rajagopalan, R., Vaucheret, H., Trejo, J. and Bartel, D.P. (2006) A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev, 20, 3407-3425. Abstract

5. Axtell, M.J., Jan, C., Rajagopalan, R. and Bartel, D.P. (2006) A Two-Hit Trigger for siRNA Biogenesis in Plants. Cell, 127, 565-577. Abstract

6. Zilberman, D., Gehring, M., Tran, R.K., Ballinger, T. and Henikoff, S. (2007) Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat Genet, 39, 61-69. Abstract

7. Xie, Z., Allen, E., Fahlgren, N., Calamar, A., Givan, S.A. and Carrington, J.C. (2005) Expression of Arabidopsis MIRNA genes. Plant Physiol, 138, 2145-2154. Abstract

8. Llave, C., Kasschau, K.D., Rector, M.A. and Carrington, J.C. (2002) Endogenous and silencing-associated small RNAs in plants. Plant Cell, 14, 1605-1619. Abstract

Arabidopsis siRNA or miRNA Papers at PubMed

Genome Data

miRBase: microRNA data http://microrna.sanger.ac.uk/

GIRI: Genetic Information Research Institute http://www.girinst.org/

NCBI: National Center for Biotechnology Information http://www.ncbi.nlm.nih.gov/

TAIR: The Arabidopsis Information Resource http://www.arabidopsis.org

JGI: DOE Joint Genome Institute http://www.jgi.doe.gov/

BioPerl:http://bioperl.org

Blast: http://www.ncbi.nlm.nih.gov/blast/

Emboss: http://emboss.sourceforge.net/

Fasta3

GMOD: http://www.gmod.org/

RepeatMasker: http://www.repeatmasker.org/

RNAfold: http://www.tbi.univie.ac.at/~ivo/RNA/