63. Nawy T, Lee J-Y, Colinas J, Wang JY, Thongrod SC, Malamy JE, Birnbaum K, Benfey PN
(2005) Transcriptional profile of the Arabidopsis root quiescent center. Plant Cell
17:1908–1925
64. Brady SM, Orlando DA, Lee JY, Wang JY,
Koch J, Dinneny JR, Mace D, Ohler U, Benfey PN (2007) A high-resolution root spatiotemporal map reveals dominant expression
patterns. Science 318:801–806
65. Dinneny JR, Long TA, Wang JY, Jung JW,
Mace D, Pointer S, Barron C, Brady SM,
Schiefelbein J, Benfey PN (2008) Cell identity
mediates the response of Arabidopsis roots to
abiotic stress. Science 320:942–945
66. Gifford ML, Dean A, Gutierrez RA, Coruzzi
GM, Birnbaum KD (2008) Cell-specific
nitrogen responses mediate developmental
plasticity. Proc Natl Acad Sci U S A
105:803–808
67. Breakfield NW, Corcoran DL, Petricka JJ,
Shen J, Sae-Seaw J, Rubio-Somoza I,
Weigel D, Ohler U, Benfey PN (2012)
High-resolution experimental and computational profiling of tissue-specific known and
novel miRNAs in Arabidopsis. Genome Res
22:163–176
68. Bruex A, Kainkaryam RM, Wieckowski Y,
Kang YH, Bernhardt C, Xia Y, Zheng XH,
Wang JY, Lee MM, Benfey P, Woolf PJ, Schiefelbein J (2012) A gene regulatory network
for root epidermis cell differentiation in Arabidopsis. PLoS Genet 8: Issue: 1 Article
Number: e1002446. https://doi.org/10.
1371/journal.pgen.1002446
69. Petricka JJ, Schauer MA, Megraw M, Breakfield NW, Thompson JW, Georgiev S, Soderblom EJ, Ohler U, Moseley MA,
Grossniklaus U, Benfey PN (2012) The protein expression landscape of the Arabidopsis
root. Proc Natl Acad Sci U S A
109:6811–6818
70. Li M, Doll J, Weckermann K, Oecking C,
Berendzen K-W, Scho ¨ffl F (2010) Detection
of in vivo interactions between Arabidopsis
class A-HSFs, using a novel BiFC fragment,
and identification of novel class B-HSF interacting proteins. Eur J Cell Biol 89:126–132
71. Li M, Berendzen K, Scho ¨ffl F (2010) Promoter specificity and interactions between
early and late Arabidopsis heat shock factors.
Plant Mol Biol 73:559–567
72. Bargmann BOR, Birnbaum KD (2009) Positive fluorescent selection permits precise,
rapid, and in-depth overexpression analysis in
plant
protoplasts.
Plant
Physiol
149:1231–1239
73. Bell PR, Helmsley AR (2000) Green plants:
their origin and diversity. Cambridge University Press, Cambridge
74. Petersson SV, Linde ´n P, Moritz T, Ljung K
(2015) Cell-type specific metabolic profiling
of Arabidopsis thaliana protoplasts as a tool
for plant systems biology. Metabolomics
11:1679–1689
75. Sparks EE, Benfey PN (2017) Tissue-specific
transcriptome profiling in arabidopsis roots.
Methods Mol Biol 1610:107–122
76. Schoft VK, Chumak N, Bindics J, Slusarz L,
Twell D, Ko ¨hler C, Tamaru H (2015) SYBR
Green-activated sorting of Arabidopsis pollen
nuclei based on different DNA/RNA content. Plant Reprod 28:61–72
77. Zheng XY, Gehring M (2019) Low-input
chromatin profiling in Arabidopsis endosperm using CUT&RUN. Plant Reprod
32:63–75
78. Rutschow HL, Baskin TI, Kramer EM (2014)
The carrier AUXIN RESISTANT (AUX1)
dominates auxin flux into Arabidopsis protoplasts. New Phytol 204:536–544
79. Santos MR, Bispo C, Becker JD (2017) Isolation of arabidopsis pollen, sperm cells, and
vegetative nuclei by fluorescence-activated
cell sorting (FACS). Methods Mol Biol
1669:193–210
80. Pontvianne F, Boyer-Clavel M, Sa ´ez-Va ´squez
J (2016) Fluorescence-activated nucleolus
sorting in Arabidopsis. Methods Mol Biol
1455:203–211
81. Nova ´k O, Antoniadi I, Ljung K (2017) Highresolution cell-type specific analysis of cytokinins in sorted root cell populations of Arabidopsis thaliana. Methods Mol Biol
1497:231–248
82. Dvor ˇa ´c ˇkova ´ M, Raposo B, Matula P, Fuchs J,
Schubert V, Pes ˇka V, Desvoyes B,
Gutierrez C, Fajkus J (2018) Replication of
ribosomal DNA in Arabidopsis occurs both
inside and outside the nucleolus during S
phase progression. J Cell Sci 131:jcs202416.
https://doi.org/10.1242/jcs.202416
83. Antoniadi I, Plac ˇkova ´ L, Simonovik B,
Dolez ˇal K, Turnbull C, Ljung K, Nova ´k O
(2015) Cell-type-specific cytokinin distribution within the arabidopsis primary root
apex. Plant Cell 27:1955–1967
84. Coker TL, Cevik V, Beynon JL, Gifford ML
(2015) Spatial dissection of the Arabidopsis
thaliana transcriptional response to downy
mildew using fluorescence activated cell sorting. Front Plant Sci 6:527. https://doi.org/
10.3389/fpls.2015.00527. eCollection 2015
Flow Cytometry and Sorting in Arabidopsis
291
(2005) Transcriptional profile of the Arabidopsis root quiescent center. Plant Cell
17:1908–1925
64. Brady SM, Orlando DA, Lee JY, Wang JY,
Koch J, Dinneny JR, Mace D, Ohler U, Benfey PN (2007) A high-resolution root spatiotemporal map reveals dominant expression
patterns. Science 318:801–806
65. Dinneny JR, Long TA, Wang JY, Jung JW,
Mace D, Pointer S, Barron C, Brady SM,
Schiefelbein J, Benfey PN (2008) Cell identity
mediates the response of Arabidopsis roots to
abiotic stress. Science 320:942–945
66. Gifford ML, Dean A, Gutierrez RA, Coruzzi
GM, Birnbaum KD (2008) Cell-specific
nitrogen responses mediate developmental
plasticity. Proc Natl Acad Sci U S A
105:803–808
67. Breakfield NW, Corcoran DL, Petricka JJ,
Shen J, Sae-Seaw J, Rubio-Somoza I,
Weigel D, Ohler U, Benfey PN (2012)
High-resolution experimental and computational profiling of tissue-specific known and
novel miRNAs in Arabidopsis. Genome Res
22:163–176
68. Bruex A, Kainkaryam RM, Wieckowski Y,
Kang YH, Bernhardt C, Xia Y, Zheng XH,
Wang JY, Lee MM, Benfey P, Woolf PJ, Schiefelbein J (2012) A gene regulatory network
for root epidermis cell differentiation in Arabidopsis. PLoS Genet 8: Issue: 1 Article
Number: e1002446. https://doi.org/10.
1371/journal.pgen.1002446
69. Petricka JJ, Schauer MA, Megraw M, Breakfield NW, Thompson JW, Georgiev S, Soderblom EJ, Ohler U, Moseley MA,
Grossniklaus U, Benfey PN (2012) The protein expression landscape of the Arabidopsis
root. Proc Natl Acad Sci U S A
109:6811–6818
70. Li M, Doll J, Weckermann K, Oecking C,
Berendzen K-W, Scho ¨ffl F (2010) Detection
of in vivo interactions between Arabidopsis
class A-HSFs, using a novel BiFC fragment,
and identification of novel class B-HSF interacting proteins. Eur J Cell Biol 89:126–132
71. Li M, Berendzen K, Scho ¨ffl F (2010) Promoter specificity and interactions between
early and late Arabidopsis heat shock factors.
Plant Mol Biol 73:559–567
72. Bargmann BOR, Birnbaum KD (2009) Positive fluorescent selection permits precise,
rapid, and in-depth overexpression analysis in
plant
protoplasts.
Plant
Physiol
149:1231–1239
73. Bell PR, Helmsley AR (2000) Green plants:
their origin and diversity. Cambridge University Press, Cambridge
74. Petersson SV, Linde ´n P, Moritz T, Ljung K
(2015) Cell-type specific metabolic profiling
of Arabidopsis thaliana protoplasts as a tool
for plant systems biology. Metabolomics
11:1679–1689
75. Sparks EE, Benfey PN (2017) Tissue-specific
transcriptome profiling in arabidopsis roots.
Methods Mol Biol 1610:107–122
76. Schoft VK, Chumak N, Bindics J, Slusarz L,
Twell D, Ko ¨hler C, Tamaru H (2015) SYBR
Green-activated sorting of Arabidopsis pollen
nuclei based on different DNA/RNA content. Plant Reprod 28:61–72
77. Zheng XY, Gehring M (2019) Low-input
chromatin profiling in Arabidopsis endosperm using CUT&RUN. Plant Reprod
32:63–75
78. Rutschow HL, Baskin TI, Kramer EM (2014)
The carrier AUXIN RESISTANT (AUX1)
dominates auxin flux into Arabidopsis protoplasts. New Phytol 204:536–544
79. Santos MR, Bispo C, Becker JD (2017) Isolation of arabidopsis pollen, sperm cells, and
vegetative nuclei by fluorescence-activated
cell sorting (FACS). Methods Mol Biol
1669:193–210
80. Pontvianne F, Boyer-Clavel M, Sa ´ez-Va ´squez
J (2016) Fluorescence-activated nucleolus
sorting in Arabidopsis. Methods Mol Biol
1455:203–211
81. Nova ´k O, Antoniadi I, Ljung K (2017) Highresolution cell-type specific analysis of cytokinins in sorted root cell populations of Arabidopsis thaliana. Methods Mol Biol
1497:231–248
82. Dvor ˇa ´c ˇkova ´ M, Raposo B, Matula P, Fuchs J,
Schubert V, Pes ˇka V, Desvoyes B,
Gutierrez C, Fajkus J (2018) Replication of
ribosomal DNA in Arabidopsis occurs both
inside and outside the nucleolus during S
phase progression. J Cell Sci 131:jcs202416.
https://doi.org/10.1242/jcs.202416
83. Antoniadi I, Plac ˇkova ´ L, Simonovik B,
Dolez ˇal K, Turnbull C, Ljung K, Nova ´k O
(2015) Cell-type-specific cytokinin distribution within the arabidopsis primary root
apex. Plant Cell 27:1955–1967
84. Coker TL, Cevik V, Beynon JL, Gifford ML
(2015) Spatial dissection of the Arabidopsis
thaliana transcriptional response to downy
mildew using fluorescence activated cell sorting. Front Plant Sci 6:527. https://doi.org/
10.3389/fpls.2015.00527. eCollection 2015
Flow Cytometry and Sorting in Arabidopsis
291