INDEX
A
Adipic acid dihydrazide agarose beads....... 242, 244, 248
Affinity purification of polysomes ....................... 460, 461
Agrobacterium ................................... 108, 113, 148, 159,
170, 176, 347, 349, 350, 433, 435, 442, 443
Agroinfiltration........................................... 108, 114, 117,
347, 351, 432, 433, 435, 442–444
Alexa 488............................................................ 60, 61, 64
Alexa 594......................................................................... 26
Alexa 647............................................................ 61–62, 65
Alkaline phosphatase (Fast Red) .................................4, 9,
13, 14, 16, 19, 20
Alkaline phosphatase (NBT/BCIP)..........................5, 13,
14, 16, 19, 20
APEX2 ...................... 284, 285, 289, 293, 300, 302–304
Arabidopsis ................................................... 14, 115, 147,
182, 242, 255, 260, 308, 405, 420, 454, 456
Arabidopsis seed sterilization ....................................... 420
Arabidopsis thaliana ........................................... 3, 7, 256,
257, 388, 391, 396, 405, 413–429
Arabidopsis thaliana cell culture ........................ 414, 419,
421, 427
B
Binary expression vectors....................434, 437–439, 448
Bioanalyzer analysis .............................................. 206, 209
Botrytis cinerea .................. 216, 218, 222, 223, 228, 230
Brachypodium distachyon ............................ 391, 396, 405
Broccoli (aptamer) ......................... 73–95, 106, 107, 197
C
Caenorhabiditis elegans .......................................... 24, 216
CDNA synthesis ..................................199, 212, 229, 231
Cell sorting ........................................................... 195–213
CHARGE technology...............................................88, 91
Chemical labeling of RNA............................................ 473
Clustered regularly interspaced short palindromic repeats
(CRISPR).......................................... 47, 137, 158,
331–340, 343–355, 357–370, 376, 381, 382
Corn (aptamer) .........................................................84, 87
CRISPR/Cas9 system .................................................. 331
CRISPR/dCas9 method .............................................. 353
CRISPR/MB ............................. 358, 359, 364–366, 368
CRISPR prediction tools .............................................. 335
D
Deep sequencing .................................199, 205, 206, 209
Degassing of leaf samples ............................................. 351
DFHO ......................................................... 76, 84, 86, 87
3,5-Difluoro-4-hydroxybenzylidene imidazolinone
(DFHBI) .......................76, 78, 84, 86, 89, 92, 93
Digitonin extraction....................... 38, 40, 41, 45, 46, 48
Digoxigenin.................................................................4, 23
Double-stranded RNA........................227, 307–327, 389
Drosophila .......................... 332, 333, 373–383, 456, 468
DsRNA pull-down ........................................................ 309
E
Electrophoretic blotting ............................................... 425
Endonuclease Csy4 ....................................................... 158
Endoplasmic reticulum .......................................... 35, 104
Environmental RNAi .................................................... 228
Enzymatic signal amplification ......................................... 5
F
FASTmiR technology ..................................................... 90
Fiji software ............................................................ 30, 272
FISH ........................................................... 23, 37, 38, 40,
42–44, 47, 51–67, 74, 197, 212, 343, 346–348,
352–354, 361, 364–366, 369, 370
FISH-quant ................................................ 30, 61, 62, 64,
65, 131, 132, 134, 135, 207
α-FLAG-coupled beads ....................................... 460, 461
Flock House virus ......................................................... 308
Flow cytometry .................................................... 201–205
Fluorescein-labeled double-stranded
RNAs......................................................... 216–221
Fluorescence activated cell sorter (FACS) ............. 76, 80,
81, 139, 203
Fluorescent spot distance measurements..................... 379
Fluorescent sRNAs..............................217, 218, 221–223
Fluorogens.................................................................73–95
Fo ¨rster resonance energy transfer (FRET) ................... 78,
79, 93, 94
Fungal mycelium......................................... 223, 224, 229
Fungus culture .............................................................. 228
Manfred Heinlein (ed.), RNA Tagging: Methods and Protocols, Methods in Molecular Biology, vol. 2166,
https://doi.org/10.1007/978-1-0716-0712-1, © Springer Science+Business Media, LLC, part of Springer Nature 2020
487
A
Adipic acid dihydrazide agarose beads....... 242, 244, 248
Affinity purification of polysomes ....................... 460, 461
Agrobacterium ................................... 108, 113, 148, 159,
170, 176, 347, 349, 350, 433, 435, 442, 443
Agroinfiltration........................................... 108, 114, 117,
347, 351, 432, 433, 435, 442–444
Alexa 488............................................................ 60, 61, 64
Alexa 594......................................................................... 26
Alexa 647............................................................ 61–62, 65
Alkaline phosphatase (Fast Red) .................................4, 9,
13, 14, 16, 19, 20
Alkaline phosphatase (NBT/BCIP)..........................5, 13,
14, 16, 19, 20
APEX2 ...................... 284, 285, 289, 293, 300, 302–304
Arabidopsis ................................................... 14, 115, 147,
182, 242, 255, 260, 308, 405, 420, 454, 456
Arabidopsis seed sterilization ....................................... 420
Arabidopsis thaliana ........................................... 3, 7, 256,
257, 388, 391, 396, 405, 413–429
Arabidopsis thaliana cell culture ........................ 414, 419,
421, 427
B
Binary expression vectors....................434, 437–439, 448
Bioanalyzer analysis .............................................. 206, 209
Botrytis cinerea .................. 216, 218, 222, 223, 228, 230
Brachypodium distachyon ............................ 391, 396, 405
Broccoli (aptamer) ......................... 73–95, 106, 107, 197
C
Caenorhabiditis elegans .......................................... 24, 216
CDNA synthesis ..................................199, 212, 229, 231
Cell sorting ........................................................... 195–213
CHARGE technology...............................................88, 91
Chemical labeling of RNA............................................ 473
Clustered regularly interspaced short palindromic repeats
(CRISPR).......................................... 47, 137, 158,
331–340, 343–355, 357–370, 376, 381, 382
Corn (aptamer) .........................................................84, 87
CRISPR/Cas9 system .................................................. 331
CRISPR/dCas9 method .............................................. 353
CRISPR/MB ............................. 358, 359, 364–366, 368
CRISPR prediction tools .............................................. 335
D
Deep sequencing .................................199, 205, 206, 209
Degassing of leaf samples ............................................. 351
DFHO ......................................................... 76, 84, 86, 87
3,5-Difluoro-4-hydroxybenzylidene imidazolinone
(DFHBI) .......................76, 78, 84, 86, 89, 92, 93
Digitonin extraction....................... 38, 40, 41, 45, 46, 48
Digoxigenin.................................................................4, 23
Double-stranded RNA........................227, 307–327, 389
Drosophila .......................... 332, 333, 373–383, 456, 468
DsRNA pull-down ........................................................ 309
E
Electrophoretic blotting ............................................... 425
Endonuclease Csy4 ....................................................... 158
Endoplasmic reticulum .......................................... 35, 104
Environmental RNAi .................................................... 228
Enzymatic signal amplification ......................................... 5
F
FASTmiR technology ..................................................... 90
Fiji software ............................................................ 30, 272
FISH ........................................................... 23, 37, 38, 40,
42–44, 47, 51–67, 74, 197, 212, 343, 346–348,
352–354, 361, 364–366, 369, 370
FISH-quant ................................................ 30, 61, 62, 64,
65, 131, 132, 134, 135, 207
α-FLAG-coupled beads ....................................... 460, 461
Flock House virus ......................................................... 308
Flow cytometry .................................................... 201–205
Fluorescein-labeled double-stranded
RNAs......................................................... 216–221
Fluorescence activated cell sorter (FACS) ............. 76, 80,
81, 139, 203
Fluorescent spot distance measurements..................... 379
Fluorescent sRNAs..............................217, 218, 221–223
Fluorogens.................................................................73–95
Fo ¨rster resonance energy transfer (FRET) ................... 78,
79, 93, 94
Fungal mycelium......................................... 223, 224, 229
Fungus culture .............................................................. 228
Manfred Heinlein (ed.), RNA Tagging: Methods and Protocols, Methods in Molecular Biology, vol. 2166,
https://doi.org/10.1007/978-1-0716-0712-1, © Springer Science+Business Media, LLC, part of Springer Nature 2020
487