Project description:Hairy vetch (Vicia villosa Roth) is recognized as a beneficial winter cover crop in the Midwestern U.S. DNA microarrays are used for assessing gene expression significance. The objective of the study was to identify a set of genes expressed in hairy vetch, that could be further analyzed for their potential in improving the crop. The RNA of four targets (soybean (Glycine max), hairy vetch, Vicia pannonica PI 170008, and Vicia pannonica PI 515988) were purified, labeled, and hybridized to 142 cDNA clones of biotic stress genes and gene sequences of soybean that were robotically spotted onto aminosilicated slides with duplicate spots and three arrays per slide. The microarray experiments were completed in a reference design experiment incorporating a two-dye system. The data were analyzed using the individual fluorescence intensities to fit two statistical models in a mixed model analysis of variance. In this analysis, systematic error effects were observed to account for 24% of the total variation. The use of a Bonferroni adjusted significance threshold allowed for adequate control over the number of falsely identified significant genes showing expression in the different target comparisons. We observed that 64 of the 142 gene sequences (45%) were differentially expressed in at least one of the target comparisons. Two of these expressed genes in hairy vetch encoded for a cold tolerance indicator, proline, and two other gene sequences encode for stress tolerance indicators, myo-inositol and calmodulin. A soybean cDNA microarray was used effectively to differentiate gene expression in hairy vetch. Keywords: comparative genomic hybridization (cross-species)
Project description:We deep sequenced a degradome library constructed from different soybean tissues. As a result, 19,830,257 represented 5,337,590 distinct signatures were obtained. 70.98% of the signatures were assigned to one soybean cDNA sequence and 24.05% matched with two cDNA sequences. 428 potential targets of small RNAs and 25 novel miRNA families were identified in soybean. A total of 211 potential miRNA targets including 150 conserved miRNA targets and 69 soybean-specific miRNA targets were identified. The signatures distribution on soybean primary miRNAs (pri-miRNAs) showed that most of the pri-miRNAs had the characteristic pattern of Dicer processing. The TAS3 small RNAs (siRNAs) biogenesis was conserved in soybean and nine Auxin Response Factors (ARFs) were identified as the TAS3 siRNA targets. The global identification of miRNAs targets would contribute to the functional research of the miRNA in soybean.
Project description:An expression profiling assay comparing dark-grown soybean seedlings with seedlings treated with 1 h far-red light using different organs including cotyledons, hook, and hypocotyl with the soybean cDNA 18kA and 18kB microarrays.
Project description:We deep sequenced a degradome library constructed from different soybean tissues. As a result, 19,830,257 represented 5,337,590 distinct signatures were obtained. 70.98% of the signatures were assigned to one soybean cDNA sequence and 24.05% matched with two cDNA sequences. 428 potential targets of small RNAs and 25 novel miRNA families were identified in soybean. A total of 211 potential miRNA targets including 150 conserved miRNA targets and 69 soybean-specific miRNA targets were identified. The signatures distribution on soybean primary miRNAs (pri-miRNAs) showed that most of the pri-miRNAs had the characteristic pattern of Dicer processing. The TAS3 small RNAs (siRNAs) biogenesis was conserved in soybean and nine Auxin Response Factors (ARFs) were identified as the TAS3 siRNA targets. The global identification of miRNAs targets would contribute to the functional research of the miRNA in soybean. one sample, We deep sequenced a degradome library constructed from different soybean tissues.
Project description:The purpose of this experiment was to identify any genes differentially expressed between the Soybean Near Isogenic Lines iron efficient Clark and iron inefficient IsoClark under iron sufficient hydroponic conditions. These genes would represent constituative genetic differences between the NILs. Keywords: Near Isogenic Line Comparison of Unstressed Soybean Plants
Project description:This SuperSeries is composed of the following subset Series: GSE33378: Deep sequencing of small RNAs from different tissues in soybean GSE33379: Deep sequencing of the degradome cDNA library in soybean Refer to individual Series
Project description:An expression profiling assay comparing dark-grown soybean seedlings with seedlings treated with 1 h far-red light using different organs including cotyledons, hook, and hypocotyl with the soybean cDNA 18kA and 18kB microarray. pairwise comparisons of far-red light treated samples and dark-grown samples in three organs: cotyledons, hook, and hypocotyl. Each comparison was done with 4 biological replicates with a dye swap.