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.