Gene Expression Nebulas
基于标准化流程分析的转录图谱综合数据库

Gene Expression Nebulas

多物种转录图谱整合数据库

PRJNA280872: Identification of Soybean Genes Differentially Regulated in Near Isogenic Lines Differing in Resistance to Aphid Infestation

来源: NCBI / GSE67779
提交时间: Apr 10 2015
释放时间: Apr 08 2016
最后更新时间: May 15 2019

概要: The soybean aphid, a plant sap sucking insect, is an important soybean pest in the USA causing significant yield losses. The Rag2 gene of soybean provides resistance to soybean aphid biotypes I and II. Transcriptomic analyses were performed on near isogenic lines (NILs) with the Rag2 allele for aphid resistance or rag2 for susceptibility at the Rag2 locus. Soybeans were infested with soybean aphids and leaves were collected at 0, 4, 8, 24, and 48 hours after infestation. RNA were extracted and a high throughput RNA-seq approach was used to examine mRNA expression in Rag2 and rag2 soybean leaves. The expression of ~43,000 genes was detected in both the Rag2 and rag2 leaves. Statistical analysis identified 2361 genes significantly regulated between the resistant and susceptible lines at different times after aphid infestation. Genes found up-regulated in the Rag2 line were annotated as involved in the cell wall, secondary and hormone metabolism, as well as in stress, signaling and transcriptional responses. Genes found up-regulated in the rag2 line were annotated as involved in photosynthesis and carbon metabolism. Interestingly, mRNAs of 2 genes (unknown and mitochondrial protease) located within the Rag2 locus were expressed significantly higher in the resistant genotype. The expression of the putative NBS-LRR resistant gene present in the Rag2 locus was not different between the two soybean lines. However, another NBL-LRR gene located just at the border of the Rag2 locus was and, therefore, may be involved in the differential resistance to aphid infestation exhibited by the two NIL genotypes analyzed.

项目整体设计: A total of 20 samples was analyzed. Two soybean genotypes, 5 time points and 2 biological replicates per condition were used.

GEN 数据集:
GEND000273
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方案
生长方案: The seedlings of the NILs were grown in an environment controlled greenhouse. The experimental design was a randomized complete block with four replications. For each NIL, four seeds per replicate for each of the four sampling times (0, 8, 24, 48 hrs after aphid infestation) were planted in 4-cm diameter x 15-cm deep plastic conetainers in a USDA greenhouse at Ohio Agricultural Research and Development Center (OARDC), Wooster, OH and the best two seedlings per conetainer were kept after germination. The conetainers were arranged in a rack with 8-cm x 12-cm spacing on a greenhouse bench. The greenhouse was maintained at approximately 26/22˚C day/night temperatures with 15 h light daily. The biotype 2 soybean aphids used in this study was from a growth chamber colony maintained at OARDC, Wooster, OH 34 . At the V2 growth stage, each soybean seedling was manually infested with 15 adult soybean aphids by placing the aphids on the top leaves of the seedling. For the 0 hr samples, just before infestation of seedlings with soybean aphids, the youngest unfolded leaves and the tips of two seedlings representing each replicate of each NIL were collected in a 2 ml tube and were immediately frozen in liquid nitrogen. The samples for 8, 24, and 48 h after infestation, were collected in the same manner, except that the aphids were gently removed from the tissue by using a soft paint brush before tissue collection. The aphids continued to walk away from the resistant seedlings within 12 to 24 hours of placement on the seedlings, so more aphids were added to these seedlings every 12 hrs to have at least 15 aphids per seedling at all times.
处理方案: Aphid infestation
提取方案: Total RNA were extracted using Trizol reagent according to manufacturer's instruction
建库方案: Complementary DNA libraries were built according to the manusfacturer’s instruction (mRNA sequencing, Sample preparation guide; Illumina, San Diego, CA) using 10 µg of RNA. Each library was labeled with a 4 nucleotide specific barcode ACGT, CGTT, GTAT and sequenced using a HiSeq 2000 (Illumina, San Diego, CA)
测序信息
分子类型: poly(A)+ RNA
库的片段类型: SINGLE
库的链类型: -
测序平台: ILLUMINA
测序仪型号: Illumina HiSeq 2000
链特异性: Unspecific
样本
基本信息:
样本描述:
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数据来源 GEN样本编号 GEN数据集编号 系列编号 项目编号 样本编号 样本名称 生物样本编号 样本访问号 实验访问号 释放时间 提交时间 最后更新时间 物种 种族 族裔 年龄 年龄单位 性别 来源名称 组织 细胞类型 细胞亚型 细胞系 疾病 疾病状态 发育阶段 突变/变异 表型 Condition Detail 生长方案 处理方案 提取方案 建库方案 分子类型 库的片段类型 链特异性 库的链类型 加标(Spike-In) 测序方法 测序平台 测序仪型号 细胞数 测序片段数 碱基数 平均测序片段长度_1 平均测序片段长度_2 唯一比对率 多重比对率 覆盖度
文章
Identification of Soybean Proteins and Genes Differentially Regulated in Near Isogenic Lines Differing in Resistance to Aphid Infestation.
Journal of proteome research . 2015-09-16 [PMID: 26350764]