161(5):1202–1214. doi:10.1016/j.cell.
2015.05.002
- Jaitin DA, Kenigsberg E, Keren-Shaul H, Ele-
fant N, Paul F, Zaretsky I, Mildner A, Cohen
N, Jung S, Tanay A, Amit I (2014) Massively
parallel single-cell RNA-seq for marker-free
decomposition of tissues into cell types. Sci-
ence 343(6172):776–779. doi:10.1126/sci
ence.1247651
- Zeisel A, Munoz-Manchado AB, Codeluppi
S, Lonnerberg P, La Manno G, Jureus A,
Marques S, Munguba H, He L, Betsholtz C,
Rolny C, Castelo-Branco G, Hjerling-Leffler
J, Linnarsson S (2015) Brain structure. Cell
types in the mouse cortex and hippocampus
revealed by single-cell RNA-seq. Science 347
(6226):1138–1142. doi:10.1126/science.
aaa1934
- Usoskin D, Furlan A, Islam S, Abdo H, Lon-
nerberg P, Lou D, Hjerling-Leffler J, Haegg-
strom J, Kharchenko O, Kharchenko PV,
Linnarsson S, Ernfors P (2015) Unbiased
classification of sensory neuron types by
large-scale single-cell RNA sequencing. Nat
Neurosci 18(1):145–153. doi:10.1038/nn.
3881
- Bendall SC, Davis KL, Amir el AD, Tadmor
MD, Simonds EF, Chen TJ, Shenfeld DK,
Nolan GP, Pe’er D (2014) Single-cell trajec-
tory detection uncovers progression and reg-
ulatory coordination in human B cell
development. Cell 157(3):714–725. doi:10.
1016/j.cell.2014.04.005
- Tang F, Barbacioru C, Bao S, Lee C, Nord-
man E, Wang X, Lao K, Surani MA (2010)
Tracing the derivation of embryonic stem cells
from the inner cell mass by single-cell RNA-
Seq analysis. Cell Stem Cell 6(5):468–478.
doi:10.1016/j.stem.2010.03.015
- Luo Y, Coskun V, Liang A, Yu J, Cheng L, Ge
W, Shi Z, Zhang K, Li C, Cui Y, Lin H, Luo
D, Wang J, Lin C, Dai Z, Zhu H, Zhang J, Liu
J, Liu H, deVellis J, Horvath S, Sun YE, Li S
(2015) Single-cell transcriptome analyses
reveal signals to activate dormant neural
stem cells. Cell 161(5):1175–1186. doi:10.
1016/j.cell.2015.04.001
- Achim K, Pettit JB, Saraiva LR, Gavriouch-
kina D, Larsson T, Arendt D, Marioni JC
(2015) High-throughput spatial mapping of
single-cell RNA-seq data to tissue of origin.
Nat Biotechnol 33(5):503–509. doi:10.
1038/nbt.3209
- Satija R, Farrell JA, Gennert D, Schier AF,
Regev A (2015) Spatial reconstruction of
single-cell gene expression data. Nat Biotech-
nol 33(5):495–502. doi:10.1038/nbt.3192
37. Combs PA, Eisen MB (2013) Sequencing
mRNA from cryo-slicedDrosophilaembryos
to determine genome-wide spatial patterns of
gene expression. PLoS One 8(8):e71820.
doi:10.1371/journal.pone.0071820
38. Junker JP, Noel ES, Guryev V, Peterson KA,
Shah G, Huisken J, McMahon AP, Berezikov
E, Bakkers J, van Oudenaarden A (2014)
Genome-wide RNA tomography in the zeb-
rafish embryo. Cell 159(3):662–675. doi:10.
1016/j.cell.2014.09.038
39. Stahl PL, Salmen F, Vickovic S, Lundmark A,
Navarro JF, Magnusson J, Giacomello S, Asp
M, Westholm JO, Huss M, Mollbrink A, Lin-
narsson S, Codeluppi S, Borg A, Ponten F,
Costea PI, Sahlen P, Mulder J, Bergmann O,
Lundeberg J, Frisen J (2016) Visualization
and analysis of gene expression in tissue sec-
tions by spatial transcriptomics. Science 353
(6294):78–82. doi:10.1126/science.aaf2403
40. Patel AP, Tirosh I, Trombetta JJ, Shalek AK,
Gillespie SM, Wakimoto H, Cahill DP, Nahed
BV, Curry WT, Martuza RL, Louis DN,
Rozenblatt-Rosen O, Suva ML, Regev A,
Bernstein BE (2014) Single-cell RNA-seq
highlights intratumoral heterogeneity in pri-
mary glioblastoma. Science 344
(6190):1396–1401. doi:10.1126/science.
1254257
41. Wills QF, Mead AJ (2015) Application of
single-cell genomics in cancer: promise and
challenges. Hum Mol Genet 24(R1):
R74–R84. doi:10.1093/hmg/ddv235
42. Gaspar I, Ephrussi A (2015) Strength in num-
bers: quantitative single-molecule RNA
detection assays. Wiley Interdiscip Rev Dev
Biol 4(2):135–150. doi:10.1002/wdev.170
43. Pitchiaya S, Heinicke LA, Custer TC, Walter
NG (2014) Single molecule fluorescence
approaches shed light on intracellular RNAs.
Chem Rev 114(6):3224–3265. doi:10.
1021/cr400496q
44. Femino AM, Fay FS, Fogarty K, Singer RH
(1998) Visualization of single RNA tran-
scripts in situ. Science 280(5363):585–590
45. Raj A, van den Bogaard P, Rifkin SA, van
Oudenaarden A, Tyagi S (2008) Imaging
individual mRNA molecules using multiple
singly labeled probes. Nat Methods 5
(10):877–879. doi:10.1038/nmeth.1253
46. Choi HM, Beck VA, Pierce NA (2014) Multi-
plexed in situ hybridization using hybridiza-
tion chain reaction. Zebrafish 11
(5):488–489. doi:10.1089/zeb.2014.1501
47. Shah S, Lubeck E, Schwarzkopf M, He TF,
Greenbaum A, Sohn CH, Lignell A, Choi
HM, Gradinaru V, Pierce NA, Cai L (2016)
The Secret Life of RNA 21
