分离和斑马鱼胚胎单细胞的表征
Summary
This protocol describes a method for isolating single cells from zebrafish embryos, enriching for cells of interest, capturing zebrafish cells in microfluidic based single cell multiplex systems, and assessing gene expression from single cells.
Abstract
The zebrafish (Danio rerio) is a powerful model organism to study vertebrate development. Though many aspects of zebrafish embryonic development have been described at the morphological level, little is known about the molecular basis of cellular changes that occur as the organism develops. With recent advancements in microfluidics and multiplexing technologies, it is now possible to characterize gene expression in single cells. This allows for investigation of heterogeneity between individual cells of specific cell populations to identify and classify cell subtypes, characterize intermediate states that occur during cell differentiation, and explore differential cellular responses to stimuli. This study describes a protocol to isolate viable, single cells from zebrafish embryos for high throughput multiplexing assays. This method may be rapidly applied to any zebrafish embryonic cell type with fluorescent markers. An extension of this method may also be used in combination with high throughput sequencing technologies to fully characterize the transcriptome of single cells. As proof of principle, the relative abundance of cardiac differentiation markers was assessed in isolated, single cells derived from nkx2.5 positive cardiac progenitors. By evaluation of gene expression at the single cell level and at a single time point, the data support a model in which cardiac progenitors coexist with differentiating progeny. The method and work flow described here is broadly applicable to the zebrafish research community, requiring only a labeled transgenic fish line and access to microfluidics technologies.
Introduction
细胞和分子生物学目前大多数研究是基于人群的平均水平。然而，重要的生物事件可能由这些传统的以人群为基础的分析被屏蔽，因为较小的群体可以在生物过程和疾病预后扮演着重要的角色。理解在不同的人群的基因表达在单细胞水平可以（有）导致相关的生物和临床见解1,2。关注胚胎发育研究，在细胞的人口较多，祖细胞往往代表性不足，使得它具有挑战性的检测基因表达微妙的变化，最终引发细胞命运决定3。同样地，一个单一的细胞类型可响应于微环境4具有不同的表达谱。例如，在相同的器官或在不同的器官（ 例如 ，主动脉或肾）驻地内皮细胞表现显著异质尽管共享共同morphological和功能特点5。此外，癌细胞填充相同的肿瘤还可以在单细胞水平6不同分子型材或突变。
在模型系统中，单个细胞转录组已成功确定了新的细胞群，其特征细胞分化过程中发生的中间状态，并透露差细胞对刺激7,8,9。这样的见解会被掩盖了传统的基于人口的研究。斑马鱼的胚胎是干，祖的极大充分利用的源代码，并在开发过程中探索单细胞的异质性和细胞身份的分子调控问题分化细胞。他们的高度千篇一律， 体外发育和易于遗传操作使其成为这种方法10,11极好的模型系统。具体而言，主要的限制单细胞根的解释Ë表达数据是在开发过程中新的中间细胞状态的可靠的鉴定需要组织收集9非常小心时机。这是必要的，以确保捕获的细胞之间的异质性表示在单个时间点的组织内的异质性，而不是异质由年龄依赖性细胞分化呈现的基因表达。相比小鼠，斑马鱼胚胎发育可以精确在大量的胚胎12的同步。此外，具有大的离合器的尺寸，斑马鱼的胚胎可以用作干细胞和祖细胞的丰富来源。
这个协议描述来隔离从斑马鱼胚胎细胞和使用用于QRT-PCR的基因表达分析的市售集成微流体回路（IFC）芯片和Autoprep设备系统捕获单细胞的方法。该协议可迅速移植到任何高通量测定复包括全转录组测序，使细胞的异质性13的更全面的分析。它还提供了多种优势，传统的基因表达分析。单细胞分离协议产生的FACS后高存活率，这降低了包含在下游应用中受损细胞的比例。通过使用IFC，捕获细胞可以直接观察来评估捕获速率和形态学评估细胞的健康。此外，该协议是广泛适用于斑马鱼研究界，只需要一个标有转基因鱼线，并获得微流体细胞捕获技术。
作为一个原则的证明，从心脏祖细胞衍生的单细胞分离和IFC芯片上捕获，然后心脏分化标志物的相对丰度被定量RT-PCR检测。在单细胞水平的基因表达分析表明，心脏祖细胞与各色共存ntiating后代。从心脏祖细胞的单细胞分析的洞察力可以在脊椎动物的发育过程中心脏祖细胞中的基因表达模式的异质性，这可能在传统的基于人群的分析被掩盖线索。
Protocol
Representative Results
Discussion
本文所描述的方法使用荧光蛋白的表达下的细胞类型特异性启动子的控制，以丰富从斑马鱼胚胎中的微流体辅助单细胞捕获系统中使用的心脏祖细胞群，以评估在单个心动基因的一个子集的表达细胞。只要FACS激光激发和发射能力与所选择的荧光团（多个）相容，可以使用任何荧光报道线路此方法。许多斑马鱼记者线已经存在，并且可以在少至3个月后将产生携带新颖记者转基因鱼。此外，此工作?…
Disclosures
The authors have nothing to disclose.
Acknowledgements
We thank Dr. C. Geoffrey Burns for fish stock. The authors are grateful to UNC Flow Cytometry Core Facility, UNC-CGIBD AAC core for resources enabling this project, and the ZAC facility for animal care. L.S. is supported by NIH T32 grant HL069768-13 (PI, Nobuyo Maeda). N.F. is supported by NSF Graduate Research Fellowship NSF-DGE-1144081. This study was supported by NIH P30DK034987 grant (to UNC Advanced Analytics Core), American Heart Association Scientist Development Grant 13SDG17060010 and Ellison Medical Foundation New Scholar Grant AG-NS-1064-13 (to Dr. Qian), and NIH R00 HL109079 grant (to Dr. Liu).
Materials
| Supplies | |||
| Dumont #5 forceps | Fine Science Tools | 11254-20 | For removing the chorion from embryos |
| Microcentrifuge tube 2 mL | GeneMate | C-3261-1 | |
| 40 um cell strainer | Biobasic | SP104151 | |
| 35 mm culture dish | Falcon | 351008 | |
| FACS tubes topped with 35 um cell strainer | Falcon | 352235 | |
| P1000 and tips | Rainin | 17005089 | |
| P20 and tips | Rainin | 17005091 | |
| IFC chip manufacturer's protocol | Fluidigm | 100-6117 | Version 100-6117 E1 was used in representative experiment |
| Wide bore pastuer glass pippette | VWR | 14673-010 | For transferring embryos |
| Adult wild type zebrafish | N/A | We used AB line | |
| Adult transgenic zebrafish | N/A | We used Tg(nkx2.5:ZsYellow) | |
| Name | Company | Catalog Number | Comments |
| Reagents for cell dissociation | |||
| Double distilled water | N/A | ||
| Instant Ocean Sea Salt | Instant Ocean | SS15-10 | |
| NaCl | FisherScientific | S271-3 | make stock in water and use for de-yolking buffer |
| KCl | Sigma Aldrich | P5405 | make stock in water and use for de-yolking buffer |
| NaHCO3 | Sigma Aldrich | S6014 | make stock in water and use for de-yolking buffer |
| Leibovitz's L-15 | Gibco | 21083-027 | |
| FBS | FisherScientific | 03-600-511 | Heat inactivate; any brand of FBS should be fine |
| Cell Dissociation Reagent 1 -TrypLE | Life Technologies | 12605-010 | Store at room temperature. |
| Cell Dissociation Reagent 2 – FACSmax | Genlantis | T200100 | Store -20; thaw on ice; bring to room temp before use |
| pronase (optional) | Sigma | P5147 | |
| L/D Dye – Sytox Blue | Life Technologies | S34857 | Any live/dead stain suitable for flow cytometry will work |
| Trypan Blue | Gibco | 15250-061 | |
| Name | Company | Catalog Number | Comments |
| Reagents for IFC plate use and qRT-PCR | |||
| Gene-specific probes | Probes will vary by experiment | ||
| TaqMan Probe ef1a | Life Technologies | Dr03432748_m1 | |
| TaqMan Probe gata4 | Life Technologies | Dr03443262_g1 | |
| TaqMan Probe nk2-5 | Life Technologies | Dr03074126_m1 | |
| TaqMan Probe myl7 | Life Technologies | Dr03105700_m1 | |
| TaqMan Probe vmhc | Life Technologies | Dr03431136_m1 | |
| TaqMan Probe isl1 | Life Technologies | Dr03425734_m1 | |
| TaqMan Gene Expression Master Mix | Life Technologies | 4369016 | |
| Reagents listed in IFC manufacturer's protocol | |||
| C1 Reagent Kit | Fluidigm | 100-5319 | Reagents for loading cells onto IFC plate |
| Ambion Single Cell-to-CTTM | Life Technologies | 4458237 | Reagents for reverse transcription and pre-amplification steps |
| Molecular Biology Quality Water | Corning | 46-000CM | |
| C1 IFC for PreAmp (5-10 um) | Fluidigm | 100-5757 | IFC plate for small cells |
| Name | Company | Catalog Number | Comments |
| Equipment | |||
| C1 AutoPrep machine | Fluidigm | 100-5477 | For IFC plate use |
| Hemocytometer | Sigma Aldrich | Z359629 | For counting cells and assessing cell size |
| Dissecting microscope | For removing embryos from chorion | ||
| Tissue culture microscope | For assessing single cell digestion | ||
| FACS machine | For isolating cells of interest |
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