RNA Detection

O

2’-O-methyl RNA.......................................233, 244, 245
Oocytes.....................................................11, 13, 18,164,
177–179, 184, 197, 274, 276, 282–284, 286, 349
Optimal cutting temperature (OCT)
compound......................................... 97,100, 108,
144, 146, 149, 150, 158, 159

P

Padlock probes....................................... 7,209–211, 213,
215–220, 222–228
PAR-CLIP...................................................415, 428, 429
Phi29 DNA polymerase.......................................213, 215
Phosphorothioate (PS)...............................244, 250, 251
Plasmodium falciparum................................................405
Poly(U) polymerase (PUP)...........................16,455, 459
Poly-A+RNA.................................................................122
PP7-PCP system..............................................11–14, 321
Protein–RNA interactions ........... 16,405, 427–453, 455
Proximity ligation ....................................... 60, 64, 70, 81
Psoralen.............................................................59–65, 67,
68, 70–78, 80–82
Psoralen analysis of RNA interactions and
structures (PARIS) ........................................59–83
Pumilio homology domain (PUM-HD)............. 12,338,
340–342
Puromycin...................................................269, 388, 393

Q

Quantitation...............................................165, 209, 220,
475, 482, 485, 487
Quencher.......................................................11,232–234,
243, 254, 289–296, 298, 299, 301–303

R

Ratiometric bimolecular beacon
(RBMB)...................................................232, 233,
235, 236, 238–240
Ratiometric imaging............................................244, 254
Reporter constructs...................................324, 351–353,
376, 382, 397, 398
Retinal ganglion cell (RGC)....................... 86, 87, 89, 92
Reverse transcription (RT)..................................... 70, 98,
99, 105, 115, 122, 210, 211, 219, 307, 313, 428,
429, 432, 436, 441, 451, 464, 465
RiboMethSeq...........................................................29–33,
35, 37–39, 41, 42, 44, 46, 47
Ribose methylation ......................................................... 30
Ribosomal RNA (rRNA).......................... 30, 55, 59, 475
Ribosomes........................................ 3, 85,320, 373, 386
RiboTag.....................................................................85–93

RNA affinity purification (RAP).........................474–477,

480, 481, 484–487

RNA binding proteins (RBPs) ............................... 11, 12,

14–16, 320, 324–331, 333, 338, 340, 410, 412,

413, 415, 416, 419, 425, 427, 429, 431, 434,

436, 440, 449, 455, 473–488

RNA capture............................................. 5, 16,195, 338,

406, 456, 474, 475, 482, 484–486

RNA modifications..................................... 2, 29, 59, 245

RNA polymerase ..................................................... 31, 35,

37, 295, 302, 360, 369

RNA structures...................................................3, 59, 60,

74, 77, 79, 81, 82, 263

RNA structurome ............................................................. 3

RNA tagging..............................10–12, 15, 16, 455–470

RNA-RNA interaction.............................. 74,77–79, 298

RNAscope............................................197–201, 203–207

Rolling circle amplification (RCA).....................210, 211,

213, 215, 216, 219, 223, 227

S

Saccharomices cerevisae,seeYeast

Sandwich hybridization ..............................189, 190, 440

SELEX...........................................................................292

Single molecule...................................................127, 136,

143, 163–170, 173, 174, 238

Single nucleotide polymorphism (SNP)............209–211,

213, 215–220, 222–228

Single-cell mRNA-seq.................................111, 112, 123

Single-molecules .................................................3, 6, 8, 9,

11, 13, 14, 18, 337–346, 355, 373, 376

Smart-seq2.............................................................. 95, 122

Spatial transcriptomics....................................... 5,95–124

Stable isotope labelling by amino acids

(SILAC)...................................................406, 407,

409, 410, 415, 474, 475, 477, 479, 484, 485, 487

Structured illumination ................................................169

SunTag.............................................................13, 14,386,

388, 389, 392, 393, 395, 397, 398, 400, 401, 403

Super-resolution imaging................................................. 7

Synapse................................................................... 51, 164

Systematic Evolution of Ligands by

EXponential enrichment (SELEX)...................290

T

Telomeric-repeat containing RNA

(TERRA).........................338, 340, 342, 343, 345

Thiazole orange (TO).........................260, 273, 277, 290

4-Thiouridine (4SU)..........................................406, 408,

410, 412, 415, 429

Tissue sectioning

cryosectioning......................144, 146, 150, 181, 199

RNA DETECTION:METHODS ANDPROTOCOLS

Index^491