Journal: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes

Article Title: In silico Analysis of 3′-End-Processing Signals in Aspergillus oryzae Using Expressed Sequence Tags and Genomic Sequencing Data

doi: 10.1093/dnares/dsr011

Figure Lengend Snippet: Profile of the A. oryzae poly(A) data set. ( A ) Frequency distribution of EST contigs based on the EST copy number. The EST copy number of each contig contained in the A. oryzae poly(A) data set was obtained from the A. oryzae EST database ( http://nribf2.nrib.go.jp/EST2/index.html ). Data on the total EST contigs were obtained from the study by Akao et al . ( B ) Gene expression levels determined by DNA microarray analysis. The fluorescence intensity of each gene was normalized to that of the histone H4 gene.

Article Snippet: The A. oryzae wild-type strain RIB40, which was used for genome sequencing analysis, was grown in sterilized wheat bran media (3.0 g wheat bran with 1.8 ml distilled water) at 30°C for 33 h. Total RNA extraction, mRNA preparation, and DNA microarray analysis were performed according to the methods of Tamano et al . Purified Cy3- or Cy5-labelled cDNA probes were hybridized using 12 K A. oryzae oligonucleotide microarrays (Fermlab, Tokyo, Japan).

Techniques: Gene Expression, Microarray, Fluorescence

Journal: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes

Article Title: In silico Analysis of 3′-End-Processing Signals in Aspergillus oryzae Using Expressed Sequence Tags and Genomic Sequencing Data

doi: 10.1093/dnares/dsr011

Figure Lengend Snippet: A schematic representation of the alignment of 3′-end-processing signals in A. oryzae , yeast, and plants. The arrow indicates the cleavage and polyadenylation site.

Article Snippet: The A. oryzae wild-type strain RIB40, which was used for genome sequencing analysis, was grown in sterilized wheat bran media (3.0 g wheat bran with 1.8 ml distilled water) at 30°C for 33 h. Total RNA extraction, mRNA preparation, and DNA microarray analysis were performed according to the methods of Tamano et al . Purified Cy3- or Cy5-labelled cDNA probes were hybridized using 12 K A. oryzae oligonucleotide microarrays (Fermlab, Tokyo, Japan).

Techniques:

Journal: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes

Article Title: In silico Analysis of 3′-End-Processing Signals in Aspergillus oryzae Using Expressed Sequence Tags and Genomic Sequencing Data

doi: 10.1093/dnares/dsr011

Figure Lengend Snippet: Comparison of protein factors involved in pre-mRNA 3′-end-processing between Aspergillus oryzae , yeast, plants, and human

Article Snippet: The A. oryzae wild-type strain RIB40, which was used for genome sequencing analysis, was grown in sterilized wheat bran media (3.0 g wheat bran with 1.8 ml distilled water) at 30°C for 33 h. Total RNA extraction, mRNA preparation, and DNA microarray analysis were performed according to the methods of Tamano et al . Purified Cy3- or Cy5-labelled cDNA probes were hybridized using 12 K A. oryzae oligonucleotide microarrays (Fermlab, Tokyo, Japan).

Techniques: Comparison

Journal: Journal of Experimental Botany

Article Title: Transcriptome analysis of Hpa1 Xoo transformed cotton revealed constitutive expression of genes in multiple signalling pathways related to disease resistance

doi: 10.1093/jxb/erq227

Figure Lengend Snippet: Hierarchical clustering of DEGs in leaves and roots of transgenic cotton T-34 compared with wild-type Z35 in the microarray analysis. Each column represents a single biological replicate and each row represents a differentially expressed probe set. L1, L2, and L3 represent biological replicates from leaves and R1, R2, and R3 represent biological replicates from roots. S/S represented self-to-self of Z35. The signal ratios were shown in a red–green colour scale, where red indicated up-regulation and green indicated down-regulation.

Article Snippet: The 12k cDNA microarray was conduced at CapitalBio Corp. (Beijing, China) using the method described by Shi et al. (2006) .

Techniques: Transgenic Assay, Microarray

Journal: Journal of Experimental Botany

Article Title: Transcriptome analysis of Hpa1 Xoo transformed cotton revealed constitutive expression of genes in multiple signalling pathways related to disease resistance

doi: 10.1093/jxb/erq227

Figure Lengend Snippet: Correlation coefficients of microarray hybridization with total RNA from leaves of transgenic cotton T-34 and wild-type Z35

Article Snippet: The 12k cDNA microarray was conduced at CapitalBio Corp. (Beijing, China) using the method described by Shi et al. (2006) .

Techniques: Microarray, Hybridization, Transgenic Assay

Journal: Journal of Experimental Botany

Article Title: Transcriptome analysis of Hpa1 Xoo transformed cotton revealed constitutive expression of genes in multiple signalling pathways related to disease resistance

doi: 10.1093/jxb/erq227

Figure Lengend Snippet: The functional annotation of 530 DEGs in leaves of transgenic T-34 identified in the microarray analysis ( P <0.001).

Article Snippet: The 12k cDNA microarray was conduced at CapitalBio Corp. (Beijing, China) using the method described by Shi et al. (2006) .

Techniques: Functional Assay, Transgenic Assay, Microarray