In Situ Hybridization Methods

Forebrain

Iris Söll and Giselbert Hauptmann

10 Large-Scale ISH on Mouse Brain Sections for Systematic Gene Expression Analysis in Developing Mouse Diencephalon

Tomomi Shimogori and Seth Blackshaw

11 High-Throughput In Situ Hybridization: Systematical Production of Gene Expression Data and Beyond

Lars Geffers and Gregor Eichele

PART IV: Evo-Devo

12 Analysis of Embryonic Gene Expression Patterns in the Hagfish

Yasuhiro Oisi, Osamu Kakitani, Shigeru Kuratani, and Kinya G. Ota

 

13 Gene Expression Analysis of Lamprey Embryos

Fumiaki Sugahara, Yasunori Murakami, and Shigeru Kuratani

14 Detection of mRNA and MicroRNA Expression in Basal Chordates, Amphioxus and Ascidians 

Simona Candiani, Greta Garbarino, and Mario Pestarino

15 Analysis of Gene Expression in Neurons and Synapses by Multi-Color In Situ Hybridization

Leonid L. Moroz and Andrea B. Kohn

PART V: Neurons, Neuronal Compartments, And Projections

16 Fluorescent In Situ Hybridization in Primary Hippocampal Neurons to Detect Localized mRNAs

Jacki E. Heraud-Farlow, Tejaswini Sharangdhar, and Michael A. Kiebler

17 Combining Whole-Mount In Situ Hybridization with Neuronal Tracing and Immunohistochemistry

Jeremy S. Duncan, Karen L. Elliott, Jennifer Kersigo, Brian Gray, and Bernd Fritzsch

PART VI: miRNA Detection by LNA-FISH

18 Fluorescent In-Situ Hybridization Detection of MicroRNAs in Newt Tissue Cryosections

Jamie Ian Morrison

PART VII: Multiplex Fluorescent In Situ Hybridization (MP-FISH)

19 Subcellular Transcript Localization in Drosophila Embryos and Tissues Visualized by Multiplex FISH

Julie Bergalet, Carole Iampietro, Ashley Chin, Xuan-Tam Nguyen, Sulin Oré-Rodriguez, Neal Cody, and Eric Lécuyer

20 Application of Alkaline Phosphatase-Mediated Azo Dye Staining for Dual Fluorescent In Situ Hybridization in Zebrafish

Giselbert Hauptmann, Gilbert Lauter and Iris Söll

21 Multiplex Fluorescent RNA In Situ Hybridization via RNAscope

Hongwei Wang, Nan Su, Li-Chong Wang, Xingyong Wu, Son Bui, Kuang-Jung Chang, Allissa Nielson, Hong-Thuy Vo, Yuling Luo, and Xiao-Jun Ma

PART VIII: Quantum Dot-Based Methods (QD-FISH)

22 Quantum Dot-Based In Situ Hybridization and Immunohistochemistry to Detect mRNA and Protein at Subcellular Levels, Comparison with Studies Under Electron Microscopy

Akira Matsuno, Yudo Ishii, Mineko Murakami, Katsumi Hoya, Shoko M. Yamada, Shinya Miyamoto, Jae-Hyun Son, Hajime Nishido, So Yamada, Yasutaka Suzuki, Akira Teramoto, Hirotoshi Utsunomiya, Johbu Itoh, Susumu Takekoshi, R. Yoshiyuki Osamura, Akiko Mizutani, and Hiroko Okinaga

23 Quantitative Multiplexed Quantum Dot Based In Situ Hybridisation in Formalin Fixed Paraffin Embedded Tissue

Eleni Tholouli, Judith A. Hoyland, and Richard J. Byers

24 Single and Multiplexed Fluorescent In Situ Hybridization using Quantum Dots Nanocrystals in Xenopus

Andriani Ioannou, Iro Eleftheriou, Anna Charalambous, and Paris A Skourides

PART IX: Single Molecule mRNA Detection (SM-FISH)

25 Quantitative Single Molecule mRNA Fluorescent In Situ Hybridization in C. elegans

Remco A. Mentink, Ni Ji, Alexander van Oudenaarden, and Hendrik C. Korswagen

26 In Situ Detection of Individual mRNA Molecules with Padlock Probes and Target-Primed Rolling-Circle Amplification in Fixed Mouse Brain Tissues

Thomas Hauling, Rongqin Ke, Tomasz Krzywkowski, Marco Mignardi, and Mats Nilsson     

27 Extended Multiplexed Fluorescent In Situ Hybridisation by Combinatorial Encoding of Individual Transcripts

Lars Martin Jakt and Satoko Moriwaki

PART X: Fast Fish

28 Characterizing Cellular Identity at One Cell Resolution

Amaresh K Ranjan, Mugdha V. Joglekar, and Anandwardhan A. Hardikar

29 Transglutaminase-Mediated In Situ Hybridization (TransISH) for mRNA Detection in Mammalian Tissues

Katsuyuki Miyawaki, Sumihare Noji, and Noriho Kamiya

30 ECHO-FISH for Gene Transcript Detection in Neuronal and Other Cells and Subcellular Compartments

Dan Ohtan Wang and Akimitsu Okamoto