PRJNA182292: Transcription factors and glyoxylate cycle genes prominent in the transition of soybean cotyledons to the first functional leaves of the seedling
概要: To understand the genetic mechanisms involved in the functional transition of cotyledons from non-photosynthetic storage tissue to metabolically active photosynthetic tissue during soybean seedling development, we constructed seven different RNA-Seq libraries using cotyledons from each developmental stage separately. Analysis of RNA-Seq data from different developmental stages revealed the differential expression of many genes including transcription factors. In this study, we focused on NAC and YABBY transcription factors which showed a conspicuous expression pattern during soybean seedling development. Their expression gradually increases from stage 1 to stage 4 of soybean germinating cotyledons. The highest level of expression was found at stage 4. Then it gradually decreased as the germinating cotyledons develop a mature seedling. We investigated the differential expression of NAC and YABBY regulated genes between stage 3 (before the functional transition) and stage 6 (after the functional transition) using our RNA-Seq data. Based on our RNA-Seq data, we found that 10 genes are up-regulated and 21 genes are down-regulated by NAC transcription factor. Similarly we found that 19 genes are up-regulated and 27 genes are down-regulated by YABBY transcription factor.
项目整体设计: High-throughput sequencing using Illumina HiSeq 2000 (RNA-Seq) was performed on seven developmental stages of soybean seedlings, with two biological replicates per stage.
Plants were grown in optimal greenhouse conditions. Germinating cotyledons were collected at stated days after planting
处理方案:
Tissue was fresh frozen in liquid nitrogen for 10 min and then stored at -80°C.
提取方案:
Total RNA was extracted from tissues using phenol:chloroform and a lithium chloride precipitation (Gonzalez and Vodkin 2007). Sequencing was performed by the Keck Center (University of Illinois) using an Illumina HiSeq 2000.
建库方案:
RNA libraries were prepared for sequencing using standard Illumina protocols
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:
生物条件:
实验变量:
方案:
测序信息:
质量评估:
数据来源
GEN样本编号
GEN数据集编号
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样本编号
样本名称
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释放时间
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物种
种族
族裔
年龄
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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
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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
Transcription factors and glyoxylate cycle genes prominent in the transition of soybean cotyledons to the first functional leaves of the seedling.
