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Small RNAs annotated to AthaMap
Sequence signatures derived from small RNA transcriptome analyses of different Arabidopsis thaliana tissues were used for genomic screenings. The complete lists of screening sequences are available at NCBI's GEO.
GEO Acession Reference Dataset AthaMap Identifier Tissue Number of sequences Number of genomic hits
GSE3008 Lu C, Tej SS, Luo S, Haudenschild CD, Meyers BC, Green PJ. 2005. Elucidation of the small RNA component of the transcriptome. Science 309: 1567-9. PubMed GSM65747 smallRNA(i) inflorescence 67,528 243,803
GSM65750 smallRNA(s) seedlings 42,062 159,304
GSE5228 Axtell MJ, Jan C, Rajagopalan R, Bartel DP. 2006. A two-hit trigger for siRNA biogenesis in plants. Cell. 127:565-77. PubMed
Rajagopalan R, Vaucheret H, Trejo J, Bartel DP. 2006. A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev. 20:3407-25. PubMed
GSM118372 smallRNA(fl3) flower 100,658 342,502
GSM118373 smallRNA(le3) leaf 67,663 307,180
GSM118374 smallRNA(se3) seedlings 77,937 332,590
GSM118375 smallRNA(si3) silique 141,539 470,537
GSE6682 Kasschau KD, Fahlgren N, Chapman EJ, Sullivan CM, Cumbie JS, Givan SA, Carrington JC. 2007. Genome-wide profiling and analysis of Arabidopsis siRNAs. PLoS Biol. 5:e57. PubMed
Fahlgren N, Howell MD, Kasschau KD, Chapman EJ, Sullivan CM, Cumbie JS, Givan SA, Law TF, Grant SR, Dangl JL, Carrington JC. 2007. High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes. PLoS One. 2:e219. PubMed
Howell MD, Fahlgren N, Chapman EJ, Cumbie JS, Sullivan CM, Givan SA, Kasschau KD, Carrington JC. 2007. Genome-wide analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNA- and tasiRNA-directed targeting. Plant Cell. 19:926-42. PubMed
GSM154336 smallRNA(i2) inflorescence 57,966 170,621
GSM154370 smallRNA(l2) leaf 8,112 36,084
GSM154375 smallRNA(s2) seedlings 12,718 50,962
Small RNA target genes
5,929 (GSE3008), 4,032 (GSE6682), and 7,696 (GSE5228) genes were predicted to be post-transcriptionally regulated by small RNAs since their transcribed regions are targets by at least one smallRNA in antisense orientation. 3,325 genes are common to all three datasets and a total number of 9,166 different genes are predicted targets of small RNAs in antisense orientation. The complete lists of genes predicted to be down-regulated by small RNAs can be downloaded as text files: 5929.txt; 4032.txt; 7696.txt; 3325.txt; 9166.txt.

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