Protocols
=========

This section collects public Dean Lab protocols as a categorized library. The
pages below normalize the source documents into a shared web format while
preserving the values, units, and step order from the original protocols.

Cloning and Mutagenesis
-----------------------

- :doc:`Gateway Cloning <protocols/gateway-cloning>`
- :doc:`DNA Shuffling <protocols/dna-shuffling>`
- :doc:`Error Prone PCR <protocols/error-prone-pcr>`
- :doc:`Saturated Mutagenesis <protocols/saturated-mutagenesis>`
- :doc:`Colony PCR <protocols/colony-pcr>`

Bacterial Methods
-----------------

- :doc:`Preparation of Chemically Competent Cells <protocols/chemically-competent-cells>`
- :doc:`Bacterial Electroporation <protocols/bacterial-electroporation>`
- :doc:`Bacterial Colony Fluorescence <protocols/bacterial-colony-fluorescence>`
- :doc:`Bacterial FACS <protocols/bacterial-facs>`

Protein and DNA Cleanup
-----------------------

- :doc:`Protein Solubility <protocols/protein-solubility>`
- :doc:`GST Protein Purification <protocols/gst-protein-purification>`
- :doc:`Purification of Small DNA Fragments <protocols/purification-small-dna-fragments>`
- :doc:`Ethanol Precipitation <protocols/ethanol-precipitation>`

Tissue Preparation and Clearing
-------------------------------

- :doc:`Labeling Tissue Samples <protocols/labeling-tissue-samples>`
- :doc:`BABB 2.0 Protocol <protocols/babb-2-0>`
- :doc:`Agarose Cube for Cleared Samples <protocols/agarose-cube-cleared-samples>`

Viral Production
----------------

- :doc:`Retrovirus Production <protocols/retrovirus-production>`
- :doc:`Viral Production - IMCD Cells <protocols/viral-production-imcd-cells>`

Imaging and Calibration
-----------------------

- :doc:`Coating Beads on Coverslip <protocols/coating-beads-on-coverslip>`
- :doc:`Quantum Yield Protocol <protocols/quantum-yield-protocol>`

Recipes
-------

- :doc:`Recipes <protocols/recipes>`

.. toctree::
   :hidden:
   :maxdepth: 1

   protocols/gateway-cloning
   protocols/dna-shuffling
   protocols/error-prone-pcr
   protocols/saturated-mutagenesis
   protocols/colony-pcr
   protocols/chemically-competent-cells
   protocols/bacterial-electroporation
   protocols/bacterial-colony-fluorescence
   protocols/bacterial-facs
   protocols/protein-solubility
   protocols/gst-protein-purification
   protocols/purification-small-dna-fragments
   protocols/ethanol-precipitation
   protocols/labeling-tissue-samples
   protocols/babb-2-0
   protocols/agarose-cube-cleared-samples
   protocols/retrovirus-production
   protocols/viral-production-imcd-cells
   protocols/coating-beads-on-coverslip
   protocols/quantum-yield-protocol
   protocols/recipes