Protocols, Resources, and Tools

Molecular Biology

• mRNA synthesis using mmessage mmachine T7/T3 kit

• Plasmid linearization using NEB enzymes

• Transformation of competent cells (XL10-gold ultracompetent cells)

• Platinum SuperFi Green PCR protocol template for optimization (Tm and DNA concentration)

• Fast SLIC/PCR digest (Novagen T4 polymerase) and E. Coli transformation (Zymo Mix&Go)

  • Use T4 polymerase to skip ligation step in PCR experiments

• Miraprep protocol for getting maxiprep yields from miniprep kits

• Cause and effect diagram: TEVC electrode offset error (ASQ template)

• GANTT chart for creating F31 timelines (Project Management)

Biochemistry

• Video Article for Ex vivo brain slice biotinylation

• BCA protocol

• Very nice overview on designing fluorescence polarization (FP) assays by Nathan Moerke

Electrophysiology

• A review on using HEK293 cells for patch-clamp experiments

• How to patch-clamp without mouth-pipetting

• An Introductory Guide To Patch Clamp Electrophysiology by Areles Molleman

• Protocol developed with my student Catherine Yi for digitizing TEVC recordings

  • For use with Warner OC725 amplifier and DATAQ kits, see this blog post for more information

• A guide to Ussing chamber studies by Lane L. Clarke, an overview on the ephys theory behind ussing chambers by Hongyu Li, an SOP by the UC Davis Mouse Metabolic Phenotyping Centers (adaptable for ALI cultures with minor modifications)

• The elusive Acquire and Analyze 2.3 operating manual from Physiological Instruments

Bioinformatics

• Database for Annotation, Visualization and Integrated Discovery (DAVID )

• Nice primer on PCA vs LDA vs tSNE plots for data visualization

• PaperBLAST - Find papers about a protein or its homologs via its sequence

• Synonymous Mutation Generator to generate control constructs for RNAi experiments (see this preprint)

• pLannotate - “re-annotates engineered plasmids and shows you where the fragments are” (see their paper)

• ApE - A plasmid editor (think SnapGene or Geneious but free) by M. Wayne Davis

• Poly - “A go package for engineering organisms” from Timothy Stiles, a super cool synbio tool!

• clinker - “a pipeline for easily generating publication-quality gene cluster comparison figures”

Business, Regulatory Science, Motivation, and other

• Trade secrets as defined by the Code of Federal Regulations (CFR)

• How to swim with Sharks (thanks to the Shorter lab at UPenn)

• PowerPoint from RA Capital Management on evaluating equity offers in Biotech

  • Check out their Innovator Resources page while you’re at it!

• The Entrepreneur’s Guide to a Biotech Startup by Peter Kolchinksy

• Kline’s borrowed research aphorisms (scanned jpg; text pdf)

• Phil Needleman’s Ten Commandments of Drug R&D