BuildACell/CellFree/DataRepository
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This is a table of various unpublished and published TX-TL experiments and experimental anecdotes. The purpose of this effort is to create a repository of different tests, calibrations, and best (or worst) practices regarding cell extracts so different labs don't redo similar work. Successful experiments, failed experiments, ideas that didn't quite pan out, and minor tweaks and protocol modifications (successful or not) are examples of the kinds of data appropriate for this repository.
Filling Out the Table: When entering data into the table, please fill out the basic information completely to aid in searching through the contents. The first column should include a link to a data page with more information. A major goal of this repository is to connect the greater cell-free community together so any entry without contact information to the contributor may be deleted
Data Pages: The data page can be anywhere and anything but we suggest that it includes experimental data or a description of experimental results, a protocol (or link to a protocol), information on experimental conditions such as DNA construct used, salt concentrations, temperature, reaction volume, pH, and additional information on the kind of extract used in the experiment. The simplest option for creating data pages including text and images is to make an openwetware page (this requires an openwetware account, which are free but may take about a week to be approved). For larger data sets https://osf.io/ is a free service for hosting large scientific data sets. It also requires an account, but these are free.
| Experiment Title and Link to Data Page | Contributor (with email) | Experiment Date | Extract Type and Organism (eg E. Coli S30, PURE) | Brief Comments on Experiments success, failure, etc. | Readout (Eg Plate Reader) | Upvote (By Manually increasing the counter) |
|---|---|---|---|---|---|---|
| HEPES/Sucrose Effects on deGFP Expression | Zoila Jurado (zjuradoq at caltech dot edu) | Fall 2018 | E. Coli S30 | HEPES/Sucrose buffer negativity effect the expression in TXTL reactions | Constituitive GFP Fluorescence | 0 |
| Sodium Bicarbonate Improves Extract Output | David Ortega (David dot Ortega at nottingham dot ac dot uk) | Spring 2018 | E. Coli S30 | Large increases in output fluorescence but little change in longevity | Constituitive GFP Fluorescence | 0 |
| Improving Extract Longevity and Output by Counteracting Reactive Oxygen Species (ROS) | David Ortega (David dot Ortega at nottingham dot ac dot uk) | Spring 2018 | E. Coli S30 | Low concentrations of glutathione and l-cysteine may help combat ROS and improve fluorescence. | Constituitive GFP Fluorescence | 0 |
| Prolonging Extract Life with Dialysis Membranes | William Poole (wpoole at caltech dot edu) | July 2018 | E. Coli S30 | The dialysis membranes tested seem to be toxic to extract | Constituitive GFP Fluorescence | 0 |
| Prolonging Extract Life with Energy-Rich Polyacrylamide gels | William Poole (wpoole at caltech dot edu) | August 2018 | E. Coli S30 | Improved energy-gel creation protocol and toxicity assays needed | Constitutive GFP Fluorescence | 0 |
| Optimal Extract Salt Concentration Reporter Dependent | William Poole (wpoole at caltech dot edu) | Summer 2017 | E. Coli S30 | Mg and K calibration performed on sfGFP and mScarlet-I show different optimal salt concentrations | Constitutive GFP and mScarlet Fluorescence | 0 |
| Technical Replicates of Extract from Same Culture Show Wide Variability | William Poole (wpoole at caltech dot edu) | Spring 2017 | E. Coli S30 | Extracts were made in parallel. Source of variability unknown. Decanting? French Press? | Constitutive GFP Fluorescence | 0 |
