Expression analysis of root cell types after treatment with sulfur deficient media. Arabidopsis thaliana

Cell-type specific transcriptional profiles were generated by FACS (Fluorescence Activated Cell Sorting) sorting of roots that express cell-type specific GFP-reporters. Five different GFP-reporter lines were used. FACS cell populations were isolated from roots grown under sulfur deficient conditions for 3 hours. Stress responses in plants are tightly coordinated with developmental processes, but the interaction between these pathways is poorly understood. Here we use genome-wide assays at high spatial and temporal resolution to understand the processes that lnk development and stress in the Arabidopsis root. Our meta-analysis finds little evidence for a universal stress response. Common stress responses appear to exists and, analagous to animal systems, many of them show cell-type specificity, suggesting a convergent evolutionary theme in multicellular organisms. Common stress responses may be mediated by cell identity regulators, as mutations in these genes resulted in altered responses to stress. Our results reveal surprising linkages between stress and development at cellular resolution, and show the power of multiple genome-wide datasets to elucidate biological processes. Overall design: 3 replicates for each of 5 cell types for sulfur deficient media

本研究通过荧光激活细胞分选术（Fluorescence Activated Cell Sorting，FACS）对表达细胞类型特异性绿色荧光蛋白（Green Fluorescent Protein, GFP）报告基因的拟南芥根系进行分选，以获取细胞类型特异性转录组图谱。本研究共使用5株独立的GFP报告基因株系。FACS分选获得的细胞群体取自经硫缺乏条件培养3小时的拟南芥根系。
植物的胁迫响应与发育过程紧密协同，但二者调控通路间的互作机制目前仍未得到充分解析。本研究借助高时空分辨率的全基因组检测技术，解析拟南芥根系中发育与胁迫响应的协同调控通路。本研究的荟萃分析结果显示，并不存在普适性的植物全局胁迫响应。尽管存在共通的胁迫响应通路，且与动物系统类似，其中多数通路均表现出细胞类型特异性，这提示多细胞生物存在趋同演化的保守机制。共通胁迫响应通路或由细胞身份调控因子介导：这类基因的突变会导致植物的胁迫响应发生显著改变。本研究结果在单细胞分辨率下揭示了此前未被发现的胁迫响应与发育过程之间的关联，并证实了多组全基因组数据集在解析生物学机制方面的强大效力。
实验整体设计：针对硫缺乏培养基培养的5种细胞类型，每种设置3次生物学重复。