Journal: BMC Genomics

Article Title: Identification and characterization of microRNAs in the flag leaf and developing seed of wheat ( Triticum aestivum L.)

doi: 10.1186/1471-2164-15-289

Figure Lengend Snippet: Known miRNAs identified in the five wheat sRNA libraries or tissues

Article Snippet: The EST sequences or the contigs from the wheat genome shotgun-sequence assemblies that matched to the sRNA reads were extracted from the databases and analyzed for the existence of pre-miRNA sequences that can form a hairpin secondary structure using miRNA prediction software MIREAP ( http://sourceforge.net/projects/mireap/ ), the potential new miRNAs predicted meeting the common criteria (see details in Methods).

Techniques:

Journal: BMC Genomics

Article Title: Identification and characterization of microRNAs in the flag leaf and developing seed of wheat ( Triticum aestivum L.)

doi: 10.1186/1471-2164-15-289

Figure Lengend Snippet: Summary of newly identified 55 novel miRNAs in the five wheat libraries or tissues

Article Snippet: The EST sequences or the contigs from the wheat genome shotgun-sequence assemblies that matched to the sRNA reads were extracted from the databases and analyzed for the existence of pre-miRNA sequences that can form a hairpin secondary structure using miRNA prediction software MIREAP ( http://sourceforge.net/projects/mireap/ ), the potential new miRNAs predicted meeting the common criteria (see details in Methods).

Techniques: Sequencing

Journal: BMC Genomics

Article Title: Identification and characterization of microRNAs in the flag leaf and developing seed of wheat ( Triticum aestivum L.)

doi: 10.1186/1471-2164-15-289

Figure Lengend Snippet: Comparison of the miRNA expression profiles determined by quantitative real-time RT-PCR (qPCR) and deep sequencing. a , known miRNAs; b , novel miRNAs and candidate miRNAs. In qPCR, UBQ was used as the internal reference gene, and the relative expression of each miRNA was calculated using a comparative C T (ΔΔC T ) method. The miRNA sample with the lowest C T value that corresponds to the highest expression level was selected as the calibrator, in which the expression level was set as 1.0. The relative expression levels of the same miRNA in the other four samples were then normalised by comparing with the highest one in the tested tissues. Three independent biological replicates were performed in this experiment. For each sample, qPCR was performed in triplicate. Each column represents the mean of three samples, and error bars represent the standard deviation. In deep sequencing technology, read counts for each miRNA in one sample were normalised to reads per million of total miRNA reads (RPM). The relative expression of each miRNA was calculated by setting the highest RPM of each miRNA across the five samples as 1.0, and the relative expression of the same miRNA in the other four samples was its RPM divided by the highest RPM.

Article Snippet: The EST sequences or the contigs from the wheat genome shotgun-sequence assemblies that matched to the sRNA reads were extracted from the databases and analyzed for the existence of pre-miRNA sequences that can form a hairpin secondary structure using miRNA prediction software MIREAP ( http://sourceforge.net/projects/mireap/ ), the potential new miRNAs predicted meeting the common criteria (see details in Methods).

Techniques: Comparison, Expressing, Quantitative RT-PCR, Sequencing, Standard Deviation

Journal: BMC Genomics

Article Title: Identification and characterization of microRNAs in the flag leaf and developing seed of wheat ( Triticum aestivum L.)

doi: 10.1186/1471-2164-15-289

Figure Lengend Snippet: Expression patterns of the known and the novel miRNAs based on deep-sequencing datasets. a , Known miRNAs; b , Novel miRNAs. The bars represent the scale of the relative expression levels of miRNAs (MEAN centred).

Article Snippet: The EST sequences or the contigs from the wheat genome shotgun-sequence assemblies that matched to the sRNA reads were extracted from the databases and analyzed for the existence of pre-miRNA sequences that can form a hairpin secondary structure using miRNA prediction software MIREAP ( http://sourceforge.net/projects/mireap/ ), the potential new miRNAs predicted meeting the common criteria (see details in Methods).

Techniques: Expressing, Sequencing