piRNA

lt;p>Part I: Methods to Study the Nature and Function of piRNAs in Non-Classical Organisms

1. Functional Analysis of Individual piRNAs in Aedes aegypti Cells and Embryos Using Antisense Oligonucleotides

            Rebecca Halbach and Pascal Miesen

2. CRISPR-Mediated Genome Engineering in Aedes aegypti

3. PIWI-Directed DNA Elimination for Tetrahymena Genetics

            Salman Shehzada and Kazufumi Mochizuki

4. Planarian PIWI-piRNA Interaction Analysis Using Immunoprecipitation and piRNA-Sequencing

            Makoto Kashima, Atsumi Miyata, and Norito Shibata

5. Isolation and Processing of Bovine Oocytes for Small RNA Sequencing

            Minjie Tan, Helena T.A. van Tol, and Elke F. Roovers

6. 3D Imaging and In Situ Hybridization for Uncovering the Functions of MicroRNA in Rice Anther

            Koji Koizumi and Reina Komiya

Part II: Methods to Study Roles of piRNAs in Classic Model Organisms

7. Cloning, Sequencing, and Linkage Analysis of piRNAs

            Rippei Hayashi

8. Drosophila Genetic Resources for Elucidating piRNA Pathway

            Kuniaki Saito

9. Generation of Stable Drosophila Ovarian Somatic Cell Lines Using the piggyBac System

            Chikara Takeuchi, Kensaku Murano, Mitsuru Ishikawa, Hideyuki Okano, and Yuka W. Iwasaki

Part III: Methods to Study Nuclear Regulation by Other Non-Coding RNAs

10. Whole Mount RNA FISH Combined with Immunofluorescence for Analysis of the Telomeric Ribonucleoproteins in the Drosophila Germline

            Valeriya Morgunova, Maria M. Sukhova, and Alla Kalmykova

11. CRISPR-Mediated Activation of Transposable Elements in Embryonic Stem Cells

            Akihiko Sakashita, Masaru Ariura, and Satoshi H. Namekawa

12. Method for Evaluating Effects of Non-Coding RNAs on Nucleosome Stability

            Mariko Dacher, Risa Fujita, Tomoya Kujirai, and Hitoshi Kurumizaka

13. Revisiting the Glass Treatment for Single Molecule Analysis of ncRNA Function

            Shuting Shen, Masahiro Naganuma, Yukihide Tomari, and Hisashi Tadakuma

14. Low Input Genome-Wide DNA Methylation Analysis with Minimal Library Amplification

15. Solid-Support Directional (SSD) RNA-Seq as a Companion Method to CLIP-Seq

            Abd-El Monsif Shawky, Mahmoud Dondeti, Zissimos Mourelatos, and Anastasios Vourekas

16. UPA-Seq-Based Search Method for Functional lncRNA Candidates

            Saori Yokoi and Shinichi Nakagawa

17. Large-Scale Analysis of RNA-Protein Interactions for Functional RNA Motif Discovery Using FOREST

            Emi Miyashita, Kaoru R. Komatsu, and Hirohide Saito

Part IV: Bioinformatic and Biophysical Methods to Study Non-Coding RNAs

18. Computational Methods for the Discovery and Annotation of Viral Integrations

            Umberto Palatini, Elisa Pischedda, and Mariangela Bonizzoni

19. Bioinformatics Approaches for Determining the Functional Impact of Repetitive Elements on Non-Coding RNAs

            Chao Zeng, Atsushi Takeda, Kotaro Sekine, Naoki Osato, Tsukasa Fukunaga, and Michiaki Hamada

20. Extending and Running the Mosquito Small RNA Genomics Resource Pipeline

            Gargi Dayama, Katia Bulekova, and Nelson C. Lau

21. Preparation of Non-Overlapping Transposable Elements (TE) Annotation by Interval Tree

            Shohei Kojima

22. Statistical Thermodynamics Approach for Intracellular Phase Separation

            Tomohiro Yamazaki and Tetsuya Yamamoto