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.
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GSE3008
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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
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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
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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 |
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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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