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以往的单细胞转录组图谱分析大多是停留在组织或器官的层面。4月19日，来自美国和德国两家实验小组以地中海涡虫(Schmidtea mediterranea)为研究对象，分别利用Drop-seq技术来绘制整个复杂动物的细胞图谱及建立细胞谱系。成果发表在近期的《Science》上。
1 Cell type transcriptome atlas for the planarian Schmidtea mediterranea
Science 2018-04-19 DOI:10.1126/science.aaq1736 http://www.x-mol.com/journal/paper/639178
Christopher T. Fincher, Omri Wurtzel, Thom de Hoog, Kellie M. Kravarik, Peter W. Reddien
2 Cell type atlas and lineage tree of a whole complex animal by single-cell transcriptomics
Science 2018-04-19 DOI:10.1126/science.aaq1723 http://www.x-mol.com/journal/paper/639177
Mireya Plass, Jordi Solana, F. Alexander Wolf, Salah Ayoub, Aristotelis Misios, Petar Glažar, Benedikt Obermayer, Fabian J. Theis, Christine Kocks, Nikolaus Rajewsky
在第一项研究中,怀特黑德生物医学研究所（whitehead）和麻省理工学院(MIT) 的研究人员报告称,他们基本上能够确定地中海涡虫的每种细胞的转录组.他们测序了50,000多个单细胞,并确定了至少44个不同的细胞群，以及150多个亚群。
这就像动物的基因组一样，细胞转录组数据集可以作为一种资源，不仅可推动真涡虫的研究。还可以推动其他两侧对称动物的研究。
德国Max Delbrück分子医学中心的研究人员也绘制了地中海涡虫的细胞类型图谱以及谱系树。他们测序了20,000多个单细胞，鉴定出至少51个细胞群和23个独立的细胞谱系.
研究结果证明了单细胞转录组分析对绘制和重建发育和再生生物学基本过程的重要性，这种方法将成为此领域不可缺少的工具。
地中海涡虫是一种真涡虫，成年后身体的任何部位都具有再生能力。美国的研究小组写道:"由于真涡虫组织的不断更新,基本上所有细胞谱系的所有阶段都存在于成虫体内,从多能干细胞到分化的细胞." 因此,分析整个生物体将提供一幅近乎完整的细胞类型图像.
涡虫（planarian Schmidtea mediterranea）：具有再生能力的模式生物
涡虫之所以具有如此强大的再生能力，主要原因是其体内有一种类似于人类干细胞的细胞，而且这种细胞占涡虫细胞总数的25%。涡虫具有几乎无限的再生能力，在未受损伤的情况下，它能保持自己身体健康而不会死亡。这使得它成为科学家开展再生研究的一个非常难得的模型。近年来，一系列涡虫相关的研究工具被陆续开发出来，同时国际上多个顶级科研单位均建立了以涡虫为模式生物的实验室。相关成果也已登上《自然》、《科学》等国际权威杂志。中国科学家也已从涡虫中发现了近50个参与到再生过程中的基因。
德国研究小组验证了最近报道的几种罕见细胞类型,并发现了更多细胞，而美国研究小组则认为真涡虫的细胞类型转录组上已基本达到饱和状态.
对于细胞类型聚类分析，两家都使用了一种名为Seurat的计算方法，该方法利用RNA-seq数据来推导单个细胞之间的空间关系。此外，美国研究小组还开发了一种工具来生成聚类表达数据，而德国方创建了一个可以单细胞数据的交互式访问网站。同时，将他们的方法与基于转基因或CRISPR基因扰动的高通量谱系追踪方法进行了对比。提出方法可以应用在所有能够分离和测序单细胞物种上,对于未来研究，该方法可以应用于新生干细胞及其分化轨迹的识别和其他物种中与分化有关的基因鉴定。
Drop-seq is a technology we developed to enable biologists to analyze RNA expression genome-wide in thousands of individual cells at once. We first described this in a 2015 paper in Cell. Though commercial implementations of droplet-based single-cell RNA-seq also now exist, we have made Drop-seq open-source and want to make sure that any lab can build their own system. The materials for constructing a Drop-seq setup in one’s own lab can be obtained for about $6,000. The reagents for performing Drop-seq cost about 6 cents per cell.
来源：http://mccarrolllab.com/dropseq/v
Cell type transcriptome atlas for the planarian Schmidtea mediterranea
Science ( IF 37.205 ) Pub Date : 2018-04-19 , DOI: 10.1126/science.aaq1736
Christopher T. Fincher, Omri Wurtzel, Thom de Hoog, Kellie M. Kravarik, Peter W. Reddien
The transcriptome of a cell dictates its unique cell-type biology. We used single-cell RNA sequencing to determine the transcriptomes for essentially every cell type of a complete animal: the regenerative planarian Schmidtea mediterranea. Planarians contain a diverse array of cell types, possess lineage progenitors for differentiated cells (including pluripotent stem cells), and constitutively express positional information, making them ideal for this undertaking. We generated data for 66,783 cells, defining transcriptomes for known and many previously unknown planarian cell types and for putative transition states between stem and differentiated cells. We also uncovered regionally expressed genes in muscle, which harbors positional information. Identifying the transcriptomes for potentially all cell types for many organisms should be readily attainable and is a powerful new approach to metazoan biology.
Cell type atlas and lineage tree of a whole complex animal by single-cell transcriptomics
Science ( IF 37.205 ) Pub Date : 2018-04-19 , DOI: 10.1126/science.aaq1723
Mireya Plass, Jordi Solana, F. Alexander Wolf, Salah Ayoub, Aristotelis Misios, Petar Glažar, Benedikt Obermayer, Fabian J. Theis, Christine Kocks, Nikolaus Rajewsky
Flatworms of the species Schmidtea mediterranea are immortal—adult animals contain a large pool of pluripotent stem cells that continuously differentiate to all adult cell types. Therefore, single-cell transcriptome profiling of adult animals should reveal mature and progenitor cells. By combining perturbation experiments, gene expression analysis, a computational method that predicts future cell states from the transcriptional changes, and a lineage reconstruction method, we placed all major cell types onto a single lineage tree that connects all cells to a single stem cell compartment. We characterize gene expression changes during differentiation and discover cell types important for regeneration. Our results demonstrate the importance of single-cell transcriptome analysis for mapping and reconstructing fundamental processes of developmental and regenerative biology at high resolution.
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