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

Journal: Molecular Medicine Reports

Article Title: Expression and clinical significance of circular RNA hsa_circ_0079787 in the peripheral blood of patients with axial spondyloarthritis

doi: 10.3892/mmr.2020.11520

Figure Lengend Snippet: Snippet of the detailed annotation for circRNA/miRNA interactions. Interactions of hsa_circ_0079787/hsa-miR-580-3p, hsa_circ_0079787/hsa-miR-125b-5p, hsa_circ_0079787/hsa-miR-5191, hsa_circ_0079787/hsa-miR-6830-5p and hsa_circ_0079787/hsa-miR-4694-3p are displayed. UTR, untranslated region; miRNA/miR, microRNA; circRNA/circ, circular RNA; hsa, Homo sapiens ; M, circRNA/miRNA interaction target from Arraystar's home-made miRNA target prediction software based on miRanda; T, circRNA/miRNA interaction target from Arraystar's home-made miRNA target prediction software based on TargetScan.

Article Snippet: The circRNA/miRNA interactions were predicted using Arraystar's home-made miRNA target prediction software (version 1; KangChen Bio-tech, Inc.) ( , ) based on TargetScan (version 6) ( ) and miRanda (version 3.3a) , and the differentially expressed circRNAs within all the comparisons were annotated in detail with the circRNA/miRNA interaction information.

Techniques: Software

Journal: Oncotarget

Article Title: Screening circular RNA expression patterns following focal cerebral ischemia in mice

doi: 10.18632/oncotarget.21238

Figure Lengend Snippet: The vertical axis represents the miRNA targeting pathways associated with the circRNAs, and the horizontal axis represents the –LgP pathway values. LgP was the logarithm of p-value, and p < 0.05 was considered significant.

Article Snippet: We then predicted the potential interactions between circRNAs and their target miRNAs using the Arraystar software for miRNA targets, according to the TargetScan and miRanda databases.

Techniques:

Journal: Oncotarget

Article Title: Screening circular RNA expression patterns following focal cerebral ischemia in mice

doi: 10.18632/oncotarget.21238

Figure Lengend Snippet: The network consists of the 3 circRNAs, mmu_circRNA_40001, mmu_circRNA_013120, and mmu_circRNA_40806; (green nodes), miRNAs (red) and their target genes (yellow).

Article Snippet: We then predicted the potential interactions between circRNAs and their target miRNAs using the Arraystar software for miRNA targets, according to the TargetScan and miRanda databases.

Techniques:

Journal: Poultry Science

Article Title: Exosomal circ_CCDC7/gga-miR-6568-3p/Pax7 axis accelerates the differentiation of chicken embryonic stem cells infected with subgroup J avian leukosis virus

doi: 10.1016/j.psj.2024.103898

Figure Lengend Snippet: circRNA/miRNA/mRNA network. (A) circRNA-targeted miRNA network. Green color represents the top 5 differential expressed circRNAs. Grape color represents circRNA-targeted miRNA. Orange color represents co-targeted miRNA of circRNAs. (B) miRNA-targeted mRNA network. Deep blue color represents 3 major ESC marker genes. Blue color represents gene-targeted miRNA. Orange color represents co-targeted miRNA of genes.

Article Snippet: Potential miRNA response elements for the 71 differentially expressed circRNAs were identified using customized Arraystar miRNA target prediction software based on the Targetscan algorithms and miRanda ( ).

Techniques: Marker

Journal: International Journal of Molecular Medicine

Article Title: Microarray analysis of circular RNA expression patterns in polarized macrophages

doi: 10.3892/ijmm.2017.2852

Figure Lengend Snippet: A snippet of the detailed annotation for circRNA-010231/miRNA interaction. The circRNA/miRNA interaction was predicted with Arraystar's home-made miRNA target prediction software based on TargetScan and miRanda, and the most differentially expressed circRNAs within all the comparisons were annotated in detail with the circRNA/miRNA interaction information. Binding sites of conserved miRNAs with good mirSVR scores are represented.

Article Snippet: To further facilitate the implication of our research study, we used the Arraystar's home-made miRNA target prediction software based on TargetScan ( ) and miRanda ( ) to predict circRNA/microRNA interaction.

Techniques: Software, Binding Assay

Journal: Oncotarget

Article Title: Circular RNA alterations are involved in resistance to avian leukosis virus subgroup-J-induced tumor formation in chickens

doi: 10.18632/oncotarget.16442

Figure Lengend Snippet: Yellow represents circRNAs, green represents miRNAs and pink represents miRNA target genes.

Article Snippet: CircRNA and miRNA interactions were predicted using customized Arraystar miRNA target prediction software based on TargetScan and miRanda [ , ]; the top five putative target miRNAs were identified for upregulated circRNAs in ALV-J-resistant chickens.

Techniques:

Journal: Chemical research in toxicology

Article Title: Isoprene-Derived Secondary Organic Aerosol Induces the Expression of MicroRNAs Associated with Inflammatory/Oxidative Stress Response in Lung Cells

doi: 10.1021/acs.chemrestox.9b00322

Figure Lengend Snippet: Thirty-One miRNAs Identified with Significant Differential Expression Associated with Exposure to Either IEPOX-Derived SOA or MAE-Derived SOA a

Article Snippet: Ingenuity Pathway Analysis (IPA) software miRNA Target Filter tool (Ingenuity Systems, Inc., Redwood City, CA, United States) was used to identify two comprehensive lists of computationally predicted gene targets of the miRNAs differentially expressed in response to IEPOX- and MAE-derived SOA, respectively.

Techniques: Quantitative Proteomics

Journal: Chemical research in toxicology

Article Title: Isoprene-Derived Secondary Organic Aerosol Induces the Expression of MicroRNAs Associated with Inflammatory/Oxidative Stress Response in Lung Cells

doi: 10.1021/acs.chemrestox.9b00322

Figure Lengend Snippet: Log fold changes of miRNA expression when exposed to IEPOX- or MAE-derived SOA compared to acidified sulfate aerosol control.

Article Snippet: Ingenuity Pathway Analysis (IPA) software miRNA Target Filter tool (Ingenuity Systems, Inc., Redwood City, CA, United States) was used to identify two comprehensive lists of computationally predicted gene targets of the miRNAs differentially expressed in response to IEPOX- and MAE-derived SOA, respectively.

Techniques: Expressing, Derivative Assay, Aerosol, Control