一些基本概念：
intracellular biochemical signaling pathways：胞内生化信号通路
extracellular mechanical cues： 胞外机械信号
The key mechanical machinery consists of myosin motors that enable contractile force generation and assist in cytoskeletal crosslinking, adhesion complexes that interface the cell to its external environment and enable force transmission, and polymerizing and depolymerizing actin filaments that drive forward protrusions and facilitate internal remodeling.
肌球蛋白马达，产生收缩力，细胞骨架，附着力复合物，聚合与解聚合，肌动蛋白丝。这些是实施迁移的一些核心因素。
The coordination and spatial organization of these mechanical parts are regulated by interconnected signaling pathways and feedback mechanisms, conferring cell polarity, and modulating cell migration modes and kinetics.
迁移不是随意的，之所以所有物种都具有自己统一的组织结构，是因为迁移模式是固定的。这种模式是由相互关联的信号通路调控的。
Canonical signaling molecules include Rho GTPases that modulate the activity levels of the mechanical machinery.
The chemotactic cells exhibited a higher expression of mRNA as analyzed by qRT-PCR of the migration and metastasis-associated genes RhoC and p38γ as compared to non-chemotactic cells
To do this, we compare gene expression fingerprints from 469 cells collected from the front, lead, and trail subregions of a typical cranial neural crest cell migratory stream at three developmental stages corresponding to initiation of migration from the dorsal neural tube, active migration towards and colonization of the branchial arches.
文章内容
基本概念：HHSt13、HHSt15等都是迁移的阶段，代表了不同发育阶段。neural tube (HHSt11), invasion of the paraxial mesoderm (HHSt13) and entry into the second branchial arch (HHSt15) with ~8 hr in between the stages.
1. Bulk RNA-seq analysis affirms a rich diversity of gene expression between the invasive front and remainder of the neural crest cell migratory stream
RT-qPCR analysis发现16个基因在invasive front中高度表达。为了找到一个unbiased manner，分析了invasive front and remainder的组织的基因表达差异，migratory front (5% of the stream, termed ‘Front’) and remainder of the stream (95% of the stream, termed ‘Stream’)。
2. Single-cell RNA-seq identifies gene expression variances based upon spatial position within the neural crest cell stream and temporal progression along the migratory pathway
we isolated and profiled individual cells from different stream positions at three developmental stages，分离了三个迁移阶段的细胞，invasive front (5% of the stream, termed ‘Front’), lead subregion of the stream (25% of the stream just proximal to the front, termed ‘Lead’), and remainder of the stream (70% of the stream, termed ‘Trail’)。
3. In vitro transcriptional signatures of migrating neural crest cells are distinct from any in vivo profile
we found significant differences between in vitro and in vivo RT-qPCR gene expression profiles by Euclidean clustering and dissimilarity matrix plots (McLennan et al., 2015) that might explain the lack of collective cell migration in culture. We find that 806 genes are down-regulated in neural crest cells grown in vitro；We also find 312 genes up-regulated in migrating neural crest cells in vitro。
4. Evidence for unique transcriptional signatures associated with cell subpopulations within the in vivo neural crest cell migratory stream
一张大heatmap
5. Hierarchical clustering and PCA analysis identify distinct transcriptional signatures associated with the invasive front of the neural crest migratory stream
To determine the transcriptional signatures associated with neural crest cells at the invasive front of the migratory stream
6. To determine the transcriptional signatures associated with neural crest cells at the invasive front of the migratory stream
To characterize the scRNA-seq Trailblazer transcriptional signature, we identified genes that are statistically enriched or reduced (Figure 5A and Figure 4—source data 1). A volcano plot shows that 964 genes are up-regulated (e.g., BAMBI, LUM, MMP2, GATA2, GATA4, GATA5 and GATA6) and 406 genes are down-regulated (e.g., DRAXIN, TFAP2A, TFAP2B, TFAP2C, TFAP2E and SOX10) within the Trailblazers (Figure 5A and Figure 4—source data 1).
These data suggest that neural crest cells with a Trailblazer transcriptional signature are mostly confined to the invasive front of the migratory stream. 这才是我需要的gene list
7. The scRNA-seq analysis validates some of our original 16 gene RT-qPCR trailblazer signature
8. Expression analysis by RNAscope of individual genes associated with the scRNA-seq Trailblazer transcriptional signature are not necessarily restricted to neural crest cells at the invasive front
9. Knockdown of some trailblazer genes showed changes in neural crest cell distance migrated
10. Identification of two distinct transcriptional signatures associated with neural crest cells isolated shortly after dorsal neural tube exit
11. The transcriptional signatures of lead and trail subpopulations are defined by small numbers of differentially expressed genes
参考：
Single-Cell Migration in Complex Microenvironments: Mechanics and Signaling Dynamics 综述
Single and collective cell migration: the mechanics of adhesions 综述
Single-cell Migration Chip for Chemotaxis-based Microfluidic Selection of Heterogeneous Cell Populations 介绍了几个关键的marker
Single-cell transcriptome analysis of avian neural crest migration reveals signatures of invasion and molecular transitions - eLIFE，NCC的迁移，有数据可用，trailblazer genes，做NCC的migration做得非常精了。
Functional transcriptomics of a migrating cell in Caenorhabditis elegans