Rajagopalan et al.
Rajagopalan et al. 2006
Contents of Supplementary Material
Supplementary Figure 1. Size distribution and 5′ nt identities of Arabidopsis small RNAs.
Supplementary Figure 2. Predicted homologs of miR828 in other eudicots. The EST accession (E. esula) or chromosome (P. trichocarpa) is noted. The predicted miRNA is rendered in red.
Supplementary Figure 3. Mapping of miRNA-directed cleavage using 5′ RACE.
The arrows indicate positions at which cleavage products were detected. The fraction of clones mapping to that site are indicated.
Supplementary Figure 4. Two high-ranking siRNA hotspots, with neighboring genomic annotations.
(A) Normalized abundance of siRNAs in the highest ranking hotspot.
(B) Normalized abundance of siRNAs in the third highest ranking hotspot. Colors and bars are as in Figure 6.
Supplementary Table 1. MicroRNA candidates.
Listed are small RNAs that mapped to miRNA-like foldbacks but were sequenced less than 25 times and for which the miRNA* species were not recovered.
Supplementary Table 2. Protein-coding genes with a high number of small RNA hits.
Supplementary Table 3. Sequences that did not match the genome but matched the cDNA database.
Supplementary Table 4. Small RNAs deriving from mobile elements.
Listed are the major classes of transposable elements and the hits-normalized sequence abundance of reads corresponding to each.
Supplementary Table 5. Genomic hits of sequenced small RNAs.
Supplementary Database Links. Links to online versions of Supplementary Databases 1, 2, and 3 for online browsing.
Supplementary Database 1. Small RNAs mapping to previously annotated miRNA loci.
Provided as a .zip archive; to view, unzip and open the _SUPPL-DATABASE_1.htm master file. Image files in the .zip archive are accessed from the worksheet or by opening individual files. Image files should be left in the same directory as the _SUPPL-DATABASE_1.htm master file.
To view online please visit
http://web.wi.mit.edu/bartel/pub/Supplemental%20Material/Rajagopalan2006/SD1/_SUPPL-DATABASE_1.htm
Supplementary Database 2. Small RNAs mapping to newly identified miRNA loci.
Provided as a .zip archive; to view, unzip and open the _SUPPL-DATABASE_2.htm master file. Image files in the .zip archive are accessed from the worksheet or by opening individual files. Image files should be left in the same directory as the _SUPPL-DATABASE_2.htm master file.
To view online please visit
http://web.wi.mit.edu/bartel/pub/Supplemental%20Material/Rajagopalan2006/SD2/_SUPPL-DATABASE_2.htm
Supplementary Database 3. Small RNAs mapping to Arabidopsis TAS loci.
Provided as a .zip archive; to view, unzip, and open the _SUPPL-DATABASE_3.htm master file. Image files in the .zip archive are accessed from the worksheet or by opening individual files. Image files should be left in the same directory as the _SUPPL-DATABASE_3.htm master file.
The coordinates along the six TAS loci for each matching tasiRNA are given. TAS labels are hyperlinked to illustrations of the abundance profiles of matching tasiRNAs at the locus.
To view online please visit
http://web.wi.mit.edu/bartel/pub/Supplemental%20Material/Rajagopalan2006/SD3/_SUPPL-DATABASE_3.htm
Supplementary Database 4. Predicted target genes of newly identified miRNAs.
Within each entry, the first line specifies the AGI code and the coordinates of the target site
within the cDNA sequence (given as [Start, End] from the 5' end of the cDNA). This is followed by the score of the alignment between the miRNA and its corresponding target site, along with the ratio of the minimum free energy (MFE) of the alignment when compared to that of a perfectly complementary site (Allen et al., 2005). The second line of each entry gives the gene
annotation, and the final lines of each entry display the alignment of the miRNA to the
predicted target site. All annotations and cDNA sequences are from the TAIR v6.0 build of
the A. thaliana genome.
Supplementary Materials, Methods and Text.