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

PRJNA532455: The Evolution of Gene Expression in Polyploid Wheats and Their Diploid Ancestors during Embryogenesis

来源: NCBI / GSE129695
提交时间: Apr 11 2019
释放时间: Oct 21 2019
最后更新时间: Oct 21 2019

概要: We present an atlas of global gene expression as well as the evolutionary divergence covering embryo, endosperm and seed coat development in wheats and their diploid ancestors, providing insights into the evolution of gene expression in embryogenesis and grain development of wheat species.

项目整体设计: We investigate the dynamics and evolution of gene expression throughout seven stages of embryo development (including the two cell, pre-embryo, transition, leaf early, leaf middle, leaf late and mature embryo), two stages of endosperm (transition stage endosperm and leaf late stage endosperm), and one pericarp stage (leaf early stage pericarp) across five wheat and ancestral grass species (AC -hexaploid, SF-tetraploid, DV-A genome diploid, SP-B genome diploid and TA-D genome diploid), two replicates for each stage.

GEN 数据集:
GEND000284
测序方法:
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组织:
发育阶段:
方案
生长方案: Polyploidy wheats, AC Barrie, Strong Field and diploid wheat grass (DV92) plants were grown in growth chambers under long-day conditions of 16 h light, 22°C and 8 h dark, 20 °C; light intensity: 100 to 120 μmol m-2 s-1 for whole life cycle. TA2780 and TA101132 were initially grown in a growth chamber at 22°C under long days (16h day/8h night), at the fifth-leaf stage, plants were moved into a cold room with 4°C and the long day photoperiod for one month (vernalization treatment), then move back to 16 h light, 22°C and 8 h dark, 20 °C; light intensity: 100 to 120 μmol m-2 s-1 again to complete its life cycle
处理方案: -
提取方案: Total RNA was extracted from embryo, endosperm and seed coat of wheat speciesat different development stages following the protocol of RNAqueous-Micro kit (Ambion, Catalog# 1927), two replicates for each development stage.
建库方案: The quantity of RNA isolated from early stage was insufficient for preparation of libraries for the RNA-seq experiments. Therefore the mRNA of all stages was amplified and the aRNA were used for RNA-seq analysis. The mRNA amplification was conducted according to the protocol provided in the MessageAmp aRNA kit (Ambion, Catalog# 1750). For RNA-seq profile analysis, we prepared Illumina mRNA-seq libraries using the TruSeq RNA kit (version 1, rev A), the libraries were prepared by using aRNA according to manufacturer's instruction. For HiSeq 2500 sequencing, 4 libraries were pooled per sequencing lane Libraries were prepared according to Illumina's instructions, using the TruSeq RNA v2 LT kit and sequenced on the Genome Analyzer following the manufacturer's protocols (https://www.illumina.com/documents/products/datasheets/datasheet_hiseq2500.pdf).
测序信息
分子类型: poly(A)+ RNA
库的片段类型: PAIRED
库的链类型: -
测序平台: ILLUMINA
测序仪型号: Illumina HiSeq 2500
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:
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质量评估:
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
The Transcriptional Landscape of Polyploid Wheats and Their Diploid Ancestors during Embryogenesis and Grain Development.
The Plant cell . 2019-10-18 [PMID: 31628162]