Ontology highlight
ABSTRACT:
PROVIDER: PRJNA718712 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14116751_1.fastq.gz | Fastqsanger.gz | |||
| SRR14116751_2.fastq.gz | Fastqsanger.gz | |||
| SRR14116752_1.fastq.gz | Fastqsanger.gz | |||
| SRR14116752_2.fastq.gz | Fastqsanger.gz | |||
| SRR14116753_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 18 |
Similar Datasets
Project description:CGH was used to compare structural variation among four soybean cultivars (Archer, Minsoy, Noir1 and Williams 82). Three different soybean cultivars (Archer, Minsoy and Noir1) were hybridized against the common reference genotype Williams 82. The soybean tiling array consists of 700k probes, spaced at approximately 1.1 kb intervals.
2011-05-03 | E-GEOD-28905 | biostudies-arrayexpress
Project description:Identify plant and pathogen genes differentially expressed during P. sojae infection of soybean cultivars differing in quantitative resistance, by using Affymetrix Soybean Genome Array analysis. Experiment Overall Design: RNA samples from mock-inoculated soybean tissue contain 2%-16% spike-in RNA from Phytophthora sojae mycelium grown in liquid sucrose-salts medium. Experiment Overall Design: 4 Experimental Replicates x 8 cultivars x 2 Treatments (inoculated or mock) x 2 Timepoints (72hr or 120hr) = 128 samples in total
2008-06-15 | E-GEOD-7124 | biostudies-arrayexpress
Project description:The Hydrophobic protein from soybean (HPS) locus is polymorphic among soybean cultivars and copy-number changes in the tandem array at this locus are directly correlated with expression level and seed coat luster phenotypes. Keywords: comparative genomic hybridization
2006-03-21 | GSE3810 | GEO
Project description:Oxidative stress caused by ground level ozone is a major contributor to yield loss in a number of important crop plants. Soybean (Glycine max) is especially ozone sensitive, and research into its response to oxidative stress is limited. To better understand the genetic response in soybean to oxidative stress, an RNA-seq analysis of two soybean cultivars was performed comparing an ozone intolerant cultivar and an ozone resistant cultivar after being exposed to ozone. A cursory analysis of the transcriptome data revealed differences between cultivars in the expression levels of genes previously implicated in oxidative stress responses, indicating unique cultivar-specific responses. An examination of the timing of gene responses over the course of ozone exposure showed expression of cuticle wax genes in the intolerant line over all sampled time points, whereas the tolerant line only expressed this pathway in the first time point. The ozone tolerant cultivar has a thicker leaf structure and we believe this lends a passive benefit to the plant which the intolerant cultivar is attempting to supplement via cuticle wax synthesis. These results suggest that differences in genetic responses work in concert with physiological differences to explain differences in ozone tolerance between soybean cultivars.
2016-01-21 | GSE59076 | GEO
Project description:Gene expression profiles in the bacterial pustule-resistant soybean cultivars
2014-01-23 | GSE54281 | GEO
Project description:Purpose: Soybean aphid (Aphis glycines Matsumura; SBA) is major pest of soybean (Glycine max) in the United States of America. One previous study on soybean, soybean-aphid interactions showed that avirulent (biotype 1) and virulent (biotype 2) biotypes can co-occur and potentially interact on resistant and susceptible soybean resulting induced susceptibility. The main objective of this research was to employ RNA sequencing technique to characterize the induced susceptibility effect in which initial feeding by virulent aphids can increase the suitability of avirulent aphids in both susceptible and resistant cultivars. Methods: The data in this submission come from the green house experiment using two genotypes of soybean: susceptible soybean cultivar was LD12-15838R and the resistant cultivar was LD12-15813Ra (with Rag1 gene) and two aphid populations: biotype 1 (avirulent) and biotype 2 (virulent biotype 2). RNA was extracted from the leave samples from resistant and susceptible cultivars treated with no aphids, biotype 2: biotype1 collected at day 1 and no aphids, biotype 2: biotype1 and no aphids: biotype1 at day 11 using PureLink RNA mini kit (Invitrogen, USA). RNA samples were treated with TURBOTM DNase (Invitrogen, USA) to remove any DNA contamination following the manufacturer’s instructions. Assessment of the isolated RNA integrity was performed by 1% agarose gel electrophoresis, and RNA concentration was measured by Nanodrop 2000 (Thermo Fisher Scientific, USA). Three replicates from these treatments in resistant and susceptible cultivars were pooled in equimolar concentration. RNAseq library construction was prepared using Illumina’s TruSeq Stranded mRNA Kit v1 (San Diego, CA). The libraries were quantified by QuBit dsDNA HS Assay (Life Technologies, Carlsbad, CA) and pooled in equimolar concentrations. The libraries were sequenced on an Illumina NextSeq 500 using a NextSeq 500/550 High Output Reagent Cartridge v2 (San Diego, CA) at 75 cycles. Results: A total of 10 RNA libraries were prepared and sequenced with the sequencing depth ranging from 24,779,816 to 29,72,4913. Total reads of 266,535,654 were subjected to FastQC analysis to determine the data quality using various quality metrics such as mean quality scores, per sequence quality scores, per sequence GC content, and sequence length distribution. The phred quality scores per base for all the samples were higher than 30. The GC content ranged from 45 to 46% and followed the normal distribution. After trimming, more than 99% of the reads were retained as the clean and good quality reads. Upon mapping these reads, we obtained high mapping rate ranging from 90.4% to 92.9%. Among the mapped reads, 85.8% to 91.9% reads were uniquely mapped. Conclusions: The objective of this study is to characterize the mechanism of induced susceptibility in soybean via transcriptional response study of soybean in presence of biotype 1 and biotype 2 soybean aphids using RNA-Seq. The data resulted from this study might provide insights into the interactions between soybean and soybean aphids and identify genes, their regulation and enriched pathways that may be associated with resistance or susceptibility to A. glycines.
2019-04-26 | GSE129626 | GEO
Project description:Identify plant and pathogen genes differentially expressed during P. sojae infection of soybean cultivars differing in quantitative resistance, by using Affymetrix Soybean Genome Array analysis. Keywords: genotypic variation on quantitative resistance
2007-11-09 | GSE7124 | GEO
Project description:Soybean aphids are phloem-feeding pests that can cause significant yield losses in soybean plants. Soybean aphids thrive on susceptible soybean lines but not on resistant lines. We used microarrays to characterize the soybean plant's transcriptional defense against aphids in two related cultivars, a susceptible line and a resistant line with the Rag1 aphid-resistance gene. We measured trancript levels in leaves after one and seven days of aphid infestation.
2012-01-31 | GSE35427 | GEO