nanotube-like extensions in mammalian cells.
Proc Natl Acad Sci U S A 114(46):9873–9882
14. Shurtleff MJ, Yao J, Qin Y, Nottingham RM,
Temoche-Diaz MM et al (2017) Broad role for
YBX1 in defining the small noncoding RNA
composition of exosomes. Proc Natl Acad Sci
U S A 114(43):8987–8995
15. Mittelbrunn M, Gutie ´rrez-Va ´zquez C,
Villarroya-Beltri C, Gonza ´lez S, Sa ´nchezCabo F et al (2011) Unidirectional transfer of
microRNA-loaded exosomes from T cells to
antigen-presenting cells. Nat Commun 2:282
16. Villarroya-Beltri C, Gutie ´rrez-Va ´zquez C, Sa ´nchez-Madrid F, Mittelbrunn M (2013) Analysis of microRNA and protein transfer by
exosomes during an immune synapse. Methods
Mol Biol 1024:41–51
17. Jiang H, Li Z, Li X, Xia J (2015) Intercellular
transfer of messenger RNAs in multiorgan
tumorigenesis by tumor cell-derived exosomes.
Mol Med Rep 11:4657–4663
18. Valadi H, Ekstro ¨m K, Bossios A, Sjo ¨strand M,
Lee JJ, Lo ¨tvall JO (2007) Exosome-mediated
transfer of mRNAs and microRNAs is a novel
mechanism of genetic exchange between cells.
Nat Cell Biol 9:654–659
19. Ekstro ¨m K, Valadi H, Sjo ¨strand M,
Malmh€ all C, Bossios A et al (2012) Characterization of mRNA and microRNA in human
mast cell-derived exosomes and their transfer
to other mast cells and blood CD34 progenitor
cells. J Extracell Vesicles 1(10):3402
20. Eirin A, Riester SM, Zhu XY, Tang H, Evans
JM et al (2014) MicroRNA and mRNA cargo
of extracellular vesicles from porcine adipose
tissue-derived mesenchymal stem cells. Gene
551:55–64
21. Lionnet T, Czaplinski K, Darzacq X, ShavTal Y, Wells AL et al (2011) A transgenic
mouse for in vivo detection of endogenous
labeled mRNA. Nat Methods 8:165–170
22. Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion
for RNA-seq data with DESeq2. Genome Biol
15:550
23. Link for DeSeq2: https://bioconductor.org/
packages/release/bioc/html/DESeq2.html
24. Robinson MD, McCarthy DJ, Smyth GK
(2010) edgeR: a bioconductor package for differential expression analysis of digital gene
expression
data.
Bioinformatics
26
(1):139–140
25. Wu H, Wang C, Wu Z (2013) A new shrinkage
estimator for dispersion improves differential
expression detection in RNA-seq data. Biostatistics 2:232–243
26. Leng N, Kendziorski C (2019) EBSeq: An R
package for gene and isoform differential
expression analysis of RNA-seq data. R package
version 1.22.1
27. Haimovich G, Gerst JE (2018) Singlemolecule fluorescence in situ hybridization
(smFISH) for RNA detection in adherent animal cells. Bio-protocol 8(21):e3070
28. Dobin A, Gingeras TR (2016) Optimizing
RNA-Seq Mapping with STAR. Methods Mol
Biol 1415:245–262
214
Sandipan Dasgupta and Jeffrey E. Gerst
Proc Natl Acad Sci U S A 114(46):9873–9882
14. Shurtleff MJ, Yao J, Qin Y, Nottingham RM,
Temoche-Diaz MM et al (2017) Broad role for
YBX1 in defining the small noncoding RNA
composition of exosomes. Proc Natl Acad Sci
U S A 114(43):8987–8995
15. Mittelbrunn M, Gutie ´rrez-Va ´zquez C,
Villarroya-Beltri C, Gonza ´lez S, Sa ´nchezCabo F et al (2011) Unidirectional transfer of
microRNA-loaded exosomes from T cells to
antigen-presenting cells. Nat Commun 2:282
16. Villarroya-Beltri C, Gutie ´rrez-Va ´zquez C, Sa ´nchez-Madrid F, Mittelbrunn M (2013) Analysis of microRNA and protein transfer by
exosomes during an immune synapse. Methods
Mol Biol 1024:41–51
17. Jiang H, Li Z, Li X, Xia J (2015) Intercellular
transfer of messenger RNAs in multiorgan
tumorigenesis by tumor cell-derived exosomes.
Mol Med Rep 11:4657–4663
18. Valadi H, Ekstro ¨m K, Bossios A, Sjo ¨strand M,
Lee JJ, Lo ¨tvall JO (2007) Exosome-mediated
transfer of mRNAs and microRNAs is a novel
mechanism of genetic exchange between cells.
Nat Cell Biol 9:654–659
19. Ekstro ¨m K, Valadi H, Sjo ¨strand M,
Malmh€ all C, Bossios A et al (2012) Characterization of mRNA and microRNA in human
mast cell-derived exosomes and their transfer
to other mast cells and blood CD34 progenitor
cells. J Extracell Vesicles 1(10):3402
20. Eirin A, Riester SM, Zhu XY, Tang H, Evans
JM et al (2014) MicroRNA and mRNA cargo
of extracellular vesicles from porcine adipose
tissue-derived mesenchymal stem cells. Gene
551:55–64
21. Lionnet T, Czaplinski K, Darzacq X, ShavTal Y, Wells AL et al (2011) A transgenic
mouse for in vivo detection of endogenous
labeled mRNA. Nat Methods 8:165–170
22. Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion
for RNA-seq data with DESeq2. Genome Biol
15:550
23. Link for DeSeq2: https://bioconductor.org/
packages/release/bioc/html/DESeq2.html
24. Robinson MD, McCarthy DJ, Smyth GK
(2010) edgeR: a bioconductor package for differential expression analysis of digital gene
expression
data.
Bioinformatics
26
(1):139–140
25. Wu H, Wang C, Wu Z (2013) A new shrinkage
estimator for dispersion improves differential
expression detection in RNA-seq data. Biostatistics 2:232–243
26. Leng N, Kendziorski C (2019) EBSeq: An R
package for gene and isoform differential
expression analysis of RNA-seq data. R package
version 1.22.1
27. Haimovich G, Gerst JE (2018) Singlemolecule fluorescence in situ hybridization
(smFISH) for RNA detection in adherent animal cells. Bio-protocol 8(21):e3070
28. Dobin A, Gingeras TR (2016) Optimizing
RNA-Seq Mapping with STAR. Methods Mol
Biol 1415:245–262
214
Sandipan Dasgupta and Jeffrey E. Gerst