Additional file 2: Figure S1. of Generation of different sizes and classes of small RNAs in barley is locus, chromosome and/or cultivar-dependent
Creators: name: Hackenberg, Michael
name: Rueda, Antonio
name: Gustafson, Perry
name: Langridge, Peter
name: Bu-Jun Shi
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biophysics
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Neuroscience
subject: Biotechnology
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: FOS: Health sciences
subject: 110309 Infectious Diseases
subject: Plant Biology
subject: 60506 Virology

description: Growth curve of shoot area of GP and Pallas under well watered and drought treatments. The projected shoot area is the sum of pixels from the two side view images and top view image taken (projected shoot area = side view 1 + side view 2 + top view). Figure S2. Size distribution of unique reads and read counts for GP and Pallas. A. Size distribution comparison of read counts between GP and Pallas (left) and Relative read frequency (Percentage) as a function of read length for GP and Pallas (right); B. Size distribution comparison of unique reads between GP and Pallas (left) and Relative frequency of unique reads (Percentage) for GP and Pallas (right); C. Size distribution of the genome-mapped read counts between GP and Pallas (left) and Relative frequency (Percentage) of genome-mapped read counts between GP and Pallas as a function of read length (right); D. Size distribution of the genome-mapped unique reads between GP and Pallas as a function of read length (left) and Relative frequency of genome mapped unique reads between GP and Pallas as a function of read length (right). Figure S3. The percentage of RNA types for GP and Pallas. A. The percentage of RNA types using the genome-mapped read count between GP and Pallas; B. The percentage of each mapped element by the genome-mapped unique reads between GP and Pallas; C. The logarithm of the percentage of each mapped element in Pallas to the percentage of each mapped element in GP. Figure S4. The percentage of all types of sRNAs in each size of the genome-mapped reads in Pallas and in GP. Figure S5. Quantitative real-time PCR of miRNAs in leaf tissues of GP and Pallas under water and drought conditions. Total RNA samples were polyadenlyated and reverse-transcribed using the NCode™ VILO™ miRNA cDNA Synthesis Kit (Invitrogen, Carlsbad, CA). Generated cDNAs were amplified with a miRNA-specific forward primer and the RT primer under the following condition: 3 min at 95 °C followed by 45 cycles of 1 s at 95 °C, 1 s at 55 °C, 30 s at 72 °C (fluorescence reading acquired) and 15 s at 81 °C. Normalization was performed using three biological replicates and four control genes as previously described [42]. Figure S6. Overrepresented functional categories for genes targeted by GP upregulated miRNAs (A) and Pallas up-regulated miRNAs (B). For each graphic, we extracted all functional GOslim terms that were 1.5 more frequent in the target genes compared to the background (all barley genes). The relative percentage of genes with a given GOslim term is depicted. For example, around 45 % of all GP target genes (in overrepresented functional categories) are involved in ion binding while this category is absent in Pallas. Ion binding and response to stresses are the only two functional categories that are statistically significantly more frequent among GP target genes than expected by chance alone. (PDF 385 kb)