G
Gateway ............................................. 108, 109, 111, 113,
115, 159, 166, 167, 434, 446
Gene-linked RNA aptamer particle (GRAP)
display .................................................................. 81
Genome editing ......................................... 137, 331–340,
374–376, 381
Germline injections ..................................... 376, 378, 381
Green fluorescent protein (GFP) ........................... 74, 81,
88, 90, 109, 111, 113–117, 124, 126, 128, 136,
146, 153, 158, 165, 170, 171, 183, 184, 187,
196, 203, 257, 271, 272, 274, 280, 293, 308,
309, 312, 315, 318, 320, 323–326, 344–348,
351–353, 383, 432, 433, 440–442, 445, 446,
449, 454, 456
Guide RNAs ...................... 331–340, 343–355, 375, 382
H
HEK-293T cells ................................................... 132, 135
HeLa cells .................................................... 196, 271, 273
Horseradish peroxidase (HRP) .............................. 5, 286,
292, 310, 312, 316, 326, 436, 468
HPLC purification ..............................478, 481, 482, 484
Human breast carcinoma (MCF7) cells ...................... 198
Human osteosarcoma cells (U2OS) .......................37–39,
44, 196
Hybridization with radioactive probes ............... 390, 400
I
ImageJ.............................................................................. 30
Immunofluorescence (IF).46–48, 51–67, 288–290, 293,
302, 362, 365, 366
Individual nucleotide resolution and
immunoprecipitation (iCLIP) ................. 256, 257
In situ hybridization (ISH)3–20, 23–32, 36, 51, 73, 122,
138, 196, 343, 361
Integrative Genomics Viewer (IGV).......... 392, 465, 467
In vitro compartmentalization (μIVC) .......................... 76
In vitro transcription....................... 9, 18, 80, 82, 91, 92,
185–187, 190, 192, 223, 233, 474–477, 479, 480
Isolation of protoplasts ........................................ 419–423
K
Kinesin .................................................................. 269, 271
L
Labeled dsRNAs......................................... 215–224, 230,
231, 233–235, 237
Lentivirus..................................................... 131, 135, 139
Light-up aptamers....................74, 80, 81, 83, 88, 92–95
Long non-coding RNAs (lncRNAs) ...........................196,
451–455, 457, 464, 466, 467
M
Magnetic sorting .................................196, 198, 199, 205
Malachite green ......................................... 74, 75, 84, 106
Mammalian cells......................................... 24, 35–48, 52,
84, 94, 123, 124, 127–132, 135, 137, 140,
195–213, 285, 369
Mango (aptamers).............................................. 82–85, 94
Mass spectrometry ..................................... 241–252, 284,
285, 302, 308, 309, 318, 322, 323
Microporation ............................358, 361, 363, 366, 369
Microprojectile bombardment ..................................... 168
Microscopy .........................................4, 7, 13–16, 20, 32,
45, 46, 60, 66, 88, 104, 106, 109, 114, 115, 122,
132, 136, 137, 146, 151–154, 207, 236, 281,
283, 286, 290, 302, 303, 308, 313, 320, 323,
325, 346, 347, 351, 353, 354, 358, 373, 374,
421, 474
miRNA expression .............................................. 432, 433,
438–439, 443, 445, 449
Mobile mRNAs .................................................... 145–154
Molecular beacons .................................. 74, 91, 357–370
Molecular motors.........................................104, 269–281
Motif enrichment analysis............................................. 245
Mouse embryonic fibroblasts .............................. 196, 197
MS2..................................................... 103–118, 121–140,
145–154, 158, 196, 197, 199, 212, 270, 271,
374–376, 379, 382
Myosins........................................................ 106, 269, 271
N
Neurospora crassa .......................................................... 158
Nicotiana benthamiana ...................................... 105, 108,
109, 113, 114, 146, 148, 151, 152, 158, 168,
170, 346, 432
Non-coding RNAs (ncRNAs) .................... 388, 389, 451
Northern blots ......................................... 3, 52, 122, 308,
310, 311, 315, 318, 319, 387–408, 414, 419,
423, 426, 427
North-western blot .............................308, 314, 315, 318
Nuclear-localization sequence (NLS) .........................107,
114–117, 126, 146, 166, 167, 175, 176, 347, 381
O
On beads protein trypsinization................................... 294
P
PANDAN technology..................................................... 91
Paraffin embedding ......................................................... 27
Plant viruses.......................................................... 105, 307
Polyethylene glycol (PEG) ................................... 78, 259,
414, 427, 458, 462, 463, 469
Polysome extraction............................455, 458, 459, 468
488
RNA TAGGING: METHODS AND PROTOCOLS
Index
Gateway ............................................. 108, 109, 111, 113,
115, 159, 166, 167, 434, 446
Gene-linked RNA aptamer particle (GRAP)
display .................................................................. 81
Genome editing ......................................... 137, 331–340,
374–376, 381
Germline injections ..................................... 376, 378, 381
Green fluorescent protein (GFP) ........................... 74, 81,
88, 90, 109, 111, 113–117, 124, 126, 128, 136,
146, 153, 158, 165, 170, 171, 183, 184, 187,
196, 203, 257, 271, 272, 274, 280, 293, 308,
309, 312, 315, 318, 320, 323–326, 344–348,
351–353, 383, 432, 433, 440–442, 445, 446,
449, 454, 456
Guide RNAs ...................... 331–340, 343–355, 375, 382
H
HEK-293T cells ................................................... 132, 135
HeLa cells .................................................... 196, 271, 273
Horseradish peroxidase (HRP) .............................. 5, 286,
292, 310, 312, 316, 326, 436, 468
HPLC purification ..............................478, 481, 482, 484
Human breast carcinoma (MCF7) cells ...................... 198
Human osteosarcoma cells (U2OS) .......................37–39,
44, 196
Hybridization with radioactive probes ............... 390, 400
I
ImageJ.............................................................................. 30
Immunofluorescence (IF).46–48, 51–67, 288–290, 293,
302, 362, 365, 366
Individual nucleotide resolution and
immunoprecipitation (iCLIP) ................. 256, 257
In situ hybridization (ISH)3–20, 23–32, 36, 51, 73, 122,
138, 196, 343, 361
Integrative Genomics Viewer (IGV).......... 392, 465, 467
In vitro compartmentalization (μIVC) .......................... 76
In vitro transcription....................... 9, 18, 80, 82, 91, 92,
185–187, 190, 192, 223, 233, 474–477, 479, 480
Isolation of protoplasts ........................................ 419–423
K
Kinesin .................................................................. 269, 271
L
Labeled dsRNAs......................................... 215–224, 230,
231, 233–235, 237
Lentivirus..................................................... 131, 135, 139
Light-up aptamers....................74, 80, 81, 83, 88, 92–95
Long non-coding RNAs (lncRNAs) ...........................196,
451–455, 457, 464, 466, 467
M
Magnetic sorting .................................196, 198, 199, 205
Malachite green ......................................... 74, 75, 84, 106
Mammalian cells......................................... 24, 35–48, 52,
84, 94, 123, 124, 127–132, 135, 137, 140,
195–213, 285, 369
Mango (aptamers).............................................. 82–85, 94
Mass spectrometry ..................................... 241–252, 284,
285, 302, 308, 309, 318, 322, 323
Microporation ............................358, 361, 363, 366, 369
Microprojectile bombardment ..................................... 168
Microscopy .........................................4, 7, 13–16, 20, 32,
45, 46, 60, 66, 88, 104, 106, 109, 114, 115, 122,
132, 136, 137, 146, 151–154, 207, 236, 281,
283, 286, 290, 302, 303, 308, 313, 320, 323,
325, 346, 347, 351, 353, 354, 358, 373, 374,
421, 474
miRNA expression .............................................. 432, 433,
438–439, 443, 445, 449
Mobile mRNAs .................................................... 145–154
Molecular beacons .................................. 74, 91, 357–370
Molecular motors.........................................104, 269–281
Motif enrichment analysis............................................. 245
Mouse embryonic fibroblasts .............................. 196, 197
MS2..................................................... 103–118, 121–140,
145–154, 158, 196, 197, 199, 212, 270, 271,
374–376, 379, 382
Myosins........................................................ 106, 269, 271
N
Neurospora crassa .......................................................... 158
Nicotiana benthamiana ...................................... 105, 108,
109, 113, 114, 146, 148, 151, 152, 158, 168,
170, 346, 432
Non-coding RNAs (ncRNAs) .................... 388, 389, 451
Northern blots ......................................... 3, 52, 122, 308,
310, 311, 315, 318, 319, 387–408, 414, 419,
423, 426, 427
North-western blot .............................308, 314, 315, 318
Nuclear-localization sequence (NLS) .........................107,
114–117, 126, 146, 166, 167, 175, 176, 347, 381
O
On beads protein trypsinization................................... 294
P
PANDAN technology..................................................... 91
Paraffin embedding ......................................................... 27
Plant viruses.......................................................... 105, 307
Polyethylene glycol (PEG) ................................... 78, 259,
414, 427, 458, 462, 463, 469
Polysome extraction............................455, 458, 459, 468
488
RNA TAGGING: METHODS AND PROTOCOLS
Index