Imaging protocols

Overview papers

• “Single-Molecule Kinetics in Living Cells” by Elf et al. (2018)
• “Imaging transcriptional dynamics” by Lim et al. (2018)

Labeling protocols

1. RNA/DNA FISH

• “Single molecule RNA FISH” by Arjun Raj’s lab
• “Analysis of Single-cell Gene Transcription by RNA Fluorescent In Situ Hybridization (FISH)” by Ronander et al. (2012)
• “Robust 3D DNA FISH Using Directly Labeled Probes” by Bolland et al. (2013)

2. MS2 and PP7 labeling

• “Localization of ASH1 mRNA Particles in Living Yeast” by Bertrand et al. (1998)
• “Translational Repression and Specific RNA Binding by the Coat Protein of the Pseudomonas Phage PP7” by Lim et al. (2001)
• “Single‐Molecule mRNA Detection in Live Yeast” Lenstra et al. (2016)
• “An improved MS2 system for accurate reporting of the mRNA life cycle” by Tutucci et al. (2018)

3. Fluorescent Proteins (endogenous)

• Cloning with CRISPR/Cas9

4. Fluorescent Proteins (transfection)

• Lipofectin with plasmid

5. Halo-, CLIP- and Snap-Tag

• “HaloTag: A Novel Protein Labeling Technology for Cell Imaging and Protein Analysis” by Los et al. (2008)
• “Snap-, CLIP- and Halo-Tag Labelling of Budding Yeast Cells” by Stagge et al. (2013)

Techniques used to analysis gene regulation

1. Widefield Microscopy

2. TIRF Microscopy

• “A Guide to Structured Illumination TIRF Microscopy at High Speed with Multiple Colors” by Young et al. (2016)
• “A practical guide to single-molecule FRET” by Roy et al. (2008)
• “Transcription initiation by human RNA polymerase II visualized at single-molecule resolution” by Revyakin et al. (2012)

3. Hilo Microscopy

• “Highly inclined thin illumination enables clear single-molecule imaging in cells” by Tokunaga et al. (2008)
• “Single-molecule analysis of transcription factor binding at transcription sites in live cells” by Morisaki et al. (2014)

4. Single Molecule Tracking

• “Monitoring dynamic binding of chromatin proteins in vivo by single-molecule tracking” by Mazza et al. (2013)

5. 3D Orbital Tracking

• “Distance Measurement by Circular Scanning of the Excitation Beam in the Two-Photon Microscope” by Kis-Petokova et al. (2004)
• “3-D Particle Tracking in a Two-Photon Microscope: Application to the Study of Molecular Dynamics in Cells” by Levi et al. (2005)
• “Chromatin Dynamics in Interphase Cells Revealed by Tracking in a Two-Photon Excitation Microscope” by Levi et al. (2005)

6. MINFLUX

• “Nanometer resolution imaging and tracking of fluorescent molecules with minimal photon fluxes” by Balzarotti et al. (2017)

7. Lightsheet Microscopy

• “Optical Sectioning Deep Inside Live Embryos by Selective Plane Illumination Microscopy” by Huisken et al. (2004)
• “Single-molecule imaging of transcription factor binding to DNA in live mammalian cells” by Gebhardt et al. (2013)

8. Lattice Lightsheet Microscopy

• “Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution” by Chen et al. (2014)
• “Single Molecule Imaging in Live Embryos Using Lattice Light-Sheet Microscopy” by Mir et al. (2018)

9. Superresolution Microscopy

• “Super-resolution fight club: A broad assessment of 2D & 3D single-molecule localization microscopy software” by Sage et al.

10. DNA-PAINT

• “Nanometer‐scale Multiplexed Super‐Resolution Imaging with an Economic 3D‐DNA‐PAINT Microscope” by Auer et al. (2018)

Analysis

1. Hidden Markov Model

• “Applying Hidden Markov Models to the Analysis of Single Ion Channel Activity” by Venkataramanan et al. (2002)
• “Analysis of Single-Molecule FRET Trajectories Using Hidden Markov Modeling” by McKinney et al. (2006)
• “What is a hidden Markov model?”  by Sean R Eddy (2004)