RNA Detection

INDEX

A

Affinity purifications....................................49–57, 85–93,
405–407, 410, 412, 414, 420, 423
Alkaline fragmentation.................................................... 30
4’-Aminomethyltrioxsalen hydrochloride
(AMT)........................................63, 67, 68, 70, 81
Antibody staining................................102, 103, 160, 164
Aptamer..........................................................11,305–316
Automated cell segmentation..............................144, 157
Axons .................................................11,85–93, 167, 169
Azide-alkyne cycloaddition reaction...................359, 362
Azide-modified UTP analogs (AMUTP)...........359–370

B

Bacteria....................................11, 16, 47,289–296, 298,
299, 301–303, 355
Bioinformatics..............................50,113, 432, 449, 452
Bioorthogonal reaction.................................................359
Biotin .................................................................4, 62,177,
179, 180, 183, 430, 474, 476, 484
Blood sample...............................................191, 193, 194
BoxB-λN system........................................... 11,321, 324,
327–331, 333
Branched DNA (bDNA) ..........................................6, 209

C

Cell culture
Gag293 cells...................................................339, 341
HEK-293FT cells....................................................233
HeLa cells....................................................7, 50,244,
251, 256, 314, 315, 364, 366, 369, 389
HT1080 cells..................................................233, 236
MCF-7...................................................407, 412, 415
U2OS cells.............................................339, 343, 389
Chemical synthesis ........................................................306
Click chemistry..............................................................434
Contact quenching ....................290, 291, 299, 301, 302
Cre-recombination.............................................86, 87, 92
Cresyl violet...........................................97,101, 102, 108
Cycloheximide...................................88–90, 93, 388, 393

D

Danio rerio,seeZebrafish
Differential centrifugation............................................422

Digoxigenin (DIG).......................................................177

2-Dimensional HCR............................................189, 193

3D Structured Illumination Microscopy

(3D-SIM)........................165, 168, 169, 173, 174

Direct lysis without RNA purification .....................81, 96

Doxycycline................................................375, 377, 383,

388, 389, 392

Drosophila melanogaster,seeFruitfly

E

Electron microscopy (EM)................................... 18,129,

177, 259, 276

ELISA-like assay............................................................189

Embryos............................................ 3, 87, 96,127, 144,

164, 221, 231, 349, 402, 477

Endosomal mRNA transport......................320, 327–329

Escherichia Coli (E.coli),seeBacteria

Exciton-controlled hybridization-sensitive

fluorescent oligonucleotide probe

(ECHO)...................................................... 11, 259

Expression atlases............................................5,111–113,

115, 122

Expression plasmids...................................269, 294, 295,

298, 302, 326, 328, 342, 345

F

FIJI,seeImageJ

FISHQuant.................................................166, 171, 172

Fixation

chemical...................................................................177

freezing................................... 96,106, 110, 158, 159

Fluorescence imaging.........................................262, 265,

338–345, 400

Fluorescent in situ hybridization

(FISH).......................................................276, 321

Fluorescent oligonucleotides...............................260, 273

Fluorescent protein

split GFP................................................227, 303, 338

superfolder GFP (sfGFP)..............386, 388, 389, 399

Fluorogenic detection............................................ 10, 273

Fluorogenic oligonucleotides........................................... 5

Forced intercalation of thiazole orange

probe (FIT).........................................11,273–286

Freezing................................................................159, 224

Fruitfly...........................................................................349

Imre Gaspar (ed.),RNA Detection: Methods and Protocols, Methods in Molecular Biology,
vol. 1649, DOI 10.1007/978-1-4939-7213-5,©Springer Science+Business Media LLC 2018

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