1. Fluorescence Reporter-Based Genome-Wide RNA Interference Screening to Identify Alternative Splicing Regulators
Ashish Misra and Michael R. Green
2. Tandem Affinity Purification Approach Coupled To Mass Spectrometry to Identify Post-translational Modifications of Histones Associated with Chromatin-binding Proteins
Sophie Beyer, Philippe Robin, and Slimane Ait-Si-Ali
3. Efficient Preparation of High-Complexity ChIP-Seq Profiles from Early Xenopus Embryos
George E. Gentsch and James C Smith 4. Systematic Discovery Of Chromatin-bound Protein Complexes from ChIP-seq Datasets
Eugenia Giannopoulou and Olivier Elemento
5. Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-seq) Protocol for Zebrafish Embryos
Canan Doganli, Melissa Sandova, Sean Thomas, and Daniel Hart
6. Establishment of time- and cell-specific RNAi in Caenorhabditis elegans
Masayuki Hamakawa and Takaaki Hirotsu
7. Cell-penetrating Peptide-mediated Delivery of Cas9 Protein and Guide RNA for Genome Editing
Bharathi Suresh, Suresh Ramakrishna, and Hyongbum Kim
8. Epigenetic Analysis of Endocrine Cell Subtypes from Human Pancreatic Islets
Jia Zhang and Klaus H. Kaestner
9. eIF3 Regulation of Protein Synthesis, Tumorigenesis, and Therapeutic Response
Ji-Ye Yin, Zizheng Dong, and Jian-Ting Zhang
10. High Resolution Gene Expression Profiling of RNA Synthesis, Processing, and Decay by Metabolic Labeling of Newly Transcribed RNA using 4-thiouridine
Andrzej J. Rutkowski and Lars Dölken
11. Accurate Detection of Differential Expression and Splicing using Low-level Features
Tomi Suomi and Laura L. Elo
12. Profiling Changes in Histone Post-translational Modifications by Top-Down Mass Spectrometry
Mowei Zhou, Si Wu, David L. Stenoien, Zhaorui Zhang, Lanelle Connolly, Michael Freitag, and Ljiljana Pasa-Tolic
13. Determining if an mRNA is a Substrate of Nonsense-mediated mRNA Decay in Saccharomyces cerevisiae
Marcus J.O. Johansson
14. Optimizing In Vitro Pre-mRNA 3' Cleavage Efficiency: Reconstitution from Anion-Exchange Separated HeLa Cleavage Factors and from Adherent HeLa Cell Nuclear Extract
Mihwa Na, Susana T. Valente, and Kevin Ryan
15. Unbiased Interrogation of 3D Genome Topology using Chromosome Conformation Capture Coupled to High-throughput Sequencing (3C-Seq)
Rutger W.W. Brouwer, Mirjam C.G.N. van den Hout, Wilfred F.J. van IJcken, Eric Soler, and Ralph Stadhouders
16. Using an Inducible CRISPR-Cas9-KRAB Effector System to Dissect Transcriptional Regulation in Human Embryonic Stem Cells Krishna Mohan Parsi, Erica Hennessy, Nicola Kearns, and René Maehr
17. In vitro assay to Study Histone Ubiquitination during Transcriptional Regulation
Jogender Singh Tushir and Sanchita Bhatnagar 18. Determination of Alternate Splicing Events using Transcriptome Arrays
Rebecca S. DeVaux, Marcy Kuentzel, Jason Herschkowitz, and Sridar V. Chittur
19. Large-scale RNA Interference Screening to Identify Transcriptional Regulators of a Tumor Suppressor Gene Matteo Forloni, Thuy Ho, Lisha Sun, and Narendra Wajapeyee
20. Transcriptional Analysis-based Integrative Genomics Approach to Identify Tumor Promoting Metabolic Genes
Romi Gupta and Narendra Wajapeyee
