Steemers FJ, Adey A, Waterston RH,
Trapnell C, Shendure J (2017) Comprehensive
single-cell transcriptional profiling of a multicellular
organism.
Science
357
(6352):661–667. https://doi.org/10.1126/
science.aam8940
5. Chen J, Renia L, Ginhoux F (2018) Constructing cell lineages from single-cell transcriptomes. Mol Asp Med 59:95–113. https://doi.
org/10.1016/j.mam.2017.10.004
6. Fincher CT, Wurtzel O, de Hoog T, Kravarik
KM, Reddien PW (2018) Cell type transcriptome atlas for the planarian Schmidtea mediterranea. Science 360(6391). https://doi.org/
10.1126/science.aaq1736
7. Plass M, Solana J, Wolf FA, Ayoub S, Misios A,
Glazar P, Obermayer B, Theis FJ, Kocks C,
Rajewsky N (2018) Cell type atlas and lineage
tree of a whole complex animal by single-cell
transcriptomics. Science 360(6391). https://
doi.org/10.1126/science.aaq1723
8. Tintori SC, Osborne Nishimura E, Golden P,
Lieb JD, Goldstein B (2016) A transcriptional
lineage of the early C. elegans embryo. Dev
Cell 38(4):430–444. https://doi.org/10.
1016/j.devcel.2016.07.025
9. Han X, Wang R, Zhou Y, Fei L, Sun H, Lai S,
Saadatpour A, Zhou Z, Chen H, Ye F,
Huang D, Xu Y, Huang W, Jiang M, Jiang X,
Mao J, Chen Y, Lu C, Xie J, Fang Q, Wang Y,
Yue R, Li T, Huang H, Orkin SH, Yuan GC,
Chen M, Guo G (2018) Mapping the mouse
cell atlas by microwell-seq. Cell 172
(5):1091–1107. e1017. https://doi.org/10.
1016/j.cell.2018.02.001
10. Wagner DE, Weinreb C, Collins ZM, Briggs
JA, Megason SG, Klein AM (2018) Single-cell
mapping of gene expression landscapes and
lineage in the zebrafish embryo. Science 360
(6392):981–987. https://doi.org/10.1126/
science.aar4362
11. Karaiskos N, Wahle P, Alles J, Boltengagen A,
Ayoub S, Kipar C, Kocks C, Rajewsky N, Zinzen RP (2017) The Drosophila embryo at
single-cell transcriptome resolution. Science
358(6360):194–199.
https://doi.org/10.
1126/science.aan3235
12. Haque A, Engel J, Teichmann SA, Lonnberg T
(2017) A practical guide to single-cell RNA-sequencing for biomedical research and clinical
applications. Genome Med 9(1):75. https://
doi.org/10.1186/s13073-017-0467-4
13. Griffiths JA, Scialdone A, Marioni JC (2018)
Using single-cell genomics to understand
developmental processes and cell fate decisions.
Mol Syst Biol 14(4):e8046. https://doi.org/
10.15252/msb.20178046
14. Becht E, McInnes L, Healy J, Dutertre CA,
Kwok IWH, Ng LG, Ginhoux F, Newell EW
(2018) Dimensionality reduction for visualizing single-cell data using UMAP. Nat Biotechnol. https://www.ncbi.nlm.nih.gov/pubmed/
30531897
15. Van der Maaten L, Hinton G (2008) Visualizing data using T-SNE. J Mach Learn Res
9:2579–2605
16. Juliano C, Swartz SZ, Wessel G (2014) Isolating specific embryonic cells of the sea urchin by
FACS. Methods Mol Biol 1128:187–196.
https://doi.org/10.1007/978-1-62703-9741_12
17. Chen J, Cheung F, Shi R, Zhou H, Lu W,
Consortium CHI (2018) PBMC fixation and
processing for chromium single-cell RNA
sequencing. J Transl Med 16(1):198. https://
doi.org/10.1186/s12967-018-1578-4
18. Tang F, Barbacioru C, Wang Y, Nordman E,
Lee C, Xu N, Wang X, Bodeau J, Tuch BB,
Siddiqui A, Lao K, Surani MA (2009) mRNASeq whole-transcriptome analysis of a single
cell. Nat Methods 6(5):377–382. https://doi.
org/10.1038/nmeth.1315
19. Islam S, Kjallquist U, Moliner A, Zajac P, Fan
JB, Lonnerberg P, Linnarsson S (2011) Characterization of the single-cell transcriptional
landscape by highly multiplex RNA-seq.
Genome Res 21(7):1160–1167. https://doi.
org/10.1101/gr.110882.110
20. Islam S, Zeisel A, Joost S, La Manno G,
Zajac P, Kasper M, Lonnerberg P, Linnarsson
S (2014) Quantitative single-cell RNA-seq
with unique molecular identifiers. Nat Methods 11(2):163–166. https://doi.org/10.
1038/nmeth.2772
21. Brennecke P, Anders S, Kim JK, Kolodziejczyk
AA, Zhang X, Proserpio V, Baying B, Benes V,
Teichmann SA, Marioni JC, Heisler MG
(2013) Accounting for technical noise in
single-cell RNA-seq experiments. Nat Methods
10(11):1093–1095.
https://doi.org/10.
1038/nmeth.2645
22. Macosko EZ, Basu A, Satija R, Nemesh J,
Shekhar K, Goldman M, Tirosh I, Bialas AR,
Kamitaki N, Martersteck EM, Trombetta JJ,
Weitz DA, Sanes JR, Shalek AK, Regev A,
McCarroll SA (2015) Highly parallel genomewide expression profiling of individual cells
using
nanoliter
droplets.
Cell
161
(5):1202–1214. https://doi.org/10.1016/j.
cell.2015.05.002
23. Klein AM, Mazutis L, Akartuna I,
Tallapragada N, Veres A, Li V, Peshkin L,
Weitz DA, Kirschner MW (2015) Droplet barcoding for single-cell transcriptomics applied
Methods for in Vivo EMT at Single Cell Resolution
313
Trapnell C, Shendure J (2017) Comprehensive
single-cell transcriptional profiling of a multicellular
organism.
Science
357
(6352):661–667. https://doi.org/10.1126/
science.aam8940
5. Chen J, Renia L, Ginhoux F (2018) Constructing cell lineages from single-cell transcriptomes. Mol Asp Med 59:95–113. https://doi.
org/10.1016/j.mam.2017.10.004
6. Fincher CT, Wurtzel O, de Hoog T, Kravarik
KM, Reddien PW (2018) Cell type transcriptome atlas for the planarian Schmidtea mediterranea. Science 360(6391). https://doi.org/
10.1126/science.aaq1736
7. Plass M, Solana J, Wolf FA, Ayoub S, Misios A,
Glazar P, Obermayer B, Theis FJ, Kocks C,
Rajewsky N (2018) Cell type atlas and lineage
tree of a whole complex animal by single-cell
transcriptomics. Science 360(6391). https://
doi.org/10.1126/science.aaq1723
8. Tintori SC, Osborne Nishimura E, Golden P,
Lieb JD, Goldstein B (2016) A transcriptional
lineage of the early C. elegans embryo. Dev
Cell 38(4):430–444. https://doi.org/10.
1016/j.devcel.2016.07.025
9. Han X, Wang R, Zhou Y, Fei L, Sun H, Lai S,
Saadatpour A, Zhou Z, Chen H, Ye F,
Huang D, Xu Y, Huang W, Jiang M, Jiang X,
Mao J, Chen Y, Lu C, Xie J, Fang Q, Wang Y,
Yue R, Li T, Huang H, Orkin SH, Yuan GC,
Chen M, Guo G (2018) Mapping the mouse
cell atlas by microwell-seq. Cell 172
(5):1091–1107. e1017. https://doi.org/10.
1016/j.cell.2018.02.001
10. Wagner DE, Weinreb C, Collins ZM, Briggs
JA, Megason SG, Klein AM (2018) Single-cell
mapping of gene expression landscapes and
lineage in the zebrafish embryo. Science 360
(6392):981–987. https://doi.org/10.1126/
science.aar4362
11. Karaiskos N, Wahle P, Alles J, Boltengagen A,
Ayoub S, Kipar C, Kocks C, Rajewsky N, Zinzen RP (2017) The Drosophila embryo at
single-cell transcriptome resolution. Science
358(6360):194–199.
https://doi.org/10.
1126/science.aan3235
12. Haque A, Engel J, Teichmann SA, Lonnberg T
(2017) A practical guide to single-cell RNA-sequencing for biomedical research and clinical
applications. Genome Med 9(1):75. https://
doi.org/10.1186/s13073-017-0467-4
13. Griffiths JA, Scialdone A, Marioni JC (2018)
Using single-cell genomics to understand
developmental processes and cell fate decisions.
Mol Syst Biol 14(4):e8046. https://doi.org/
10.15252/msb.20178046
14. Becht E, McInnes L, Healy J, Dutertre CA,
Kwok IWH, Ng LG, Ginhoux F, Newell EW
(2018) Dimensionality reduction for visualizing single-cell data using UMAP. Nat Biotechnol. https://www.ncbi.nlm.nih.gov/pubmed/
30531897
15. Van der Maaten L, Hinton G (2008) Visualizing data using T-SNE. J Mach Learn Res
9:2579–2605
16. Juliano C, Swartz SZ, Wessel G (2014) Isolating specific embryonic cells of the sea urchin by
FACS. Methods Mol Biol 1128:187–196.
https://doi.org/10.1007/978-1-62703-9741_12
17. Chen J, Cheung F, Shi R, Zhou H, Lu W,
Consortium CHI (2018) PBMC fixation and
processing for chromium single-cell RNA
sequencing. J Transl Med 16(1):198. https://
doi.org/10.1186/s12967-018-1578-4
18. Tang F, Barbacioru C, Wang Y, Nordman E,
Lee C, Xu N, Wang X, Bodeau J, Tuch BB,
Siddiqui A, Lao K, Surani MA (2009) mRNASeq whole-transcriptome analysis of a single
cell. Nat Methods 6(5):377–382. https://doi.
org/10.1038/nmeth.1315
19. Islam S, Kjallquist U, Moliner A, Zajac P, Fan
JB, Lonnerberg P, Linnarsson S (2011) Characterization of the single-cell transcriptional
landscape by highly multiplex RNA-seq.
Genome Res 21(7):1160–1167. https://doi.
org/10.1101/gr.110882.110
20. Islam S, Zeisel A, Joost S, La Manno G,
Zajac P, Kasper M, Lonnerberg P, Linnarsson
S (2014) Quantitative single-cell RNA-seq
with unique molecular identifiers. Nat Methods 11(2):163–166. https://doi.org/10.
1038/nmeth.2772
21. Brennecke P, Anders S, Kim JK, Kolodziejczyk
AA, Zhang X, Proserpio V, Baying B, Benes V,
Teichmann SA, Marioni JC, Heisler MG
(2013) Accounting for technical noise in
single-cell RNA-seq experiments. Nat Methods
10(11):1093–1095.
https://doi.org/10.
1038/nmeth.2645
22. Macosko EZ, Basu A, Satija R, Nemesh J,
Shekhar K, Goldman M, Tirosh I, Bialas AR,
Kamitaki N, Martersteck EM, Trombetta JJ,
Weitz DA, Sanes JR, Shalek AK, Regev A,
McCarroll SA (2015) Highly parallel genomewide expression profiling of individual cells
using
nanoliter
droplets.
Cell
161
(5):1202–1214. https://doi.org/10.1016/j.
cell.2015.05.002
23. Klein AM, Mazutis L, Akartuna I,
Tallapragada N, Veres A, Li V, Peshkin L,
Weitz DA, Kirschner MW (2015) Droplet barcoding for single-cell transcriptomics applied
Methods for in Vivo EMT at Single Cell Resolution
313