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<h2><strong>Experimental Guidelines for Replicating Labs</strong></h2> <h2>General guidelines:</h2> <p><strong>Cell Line Authentication</strong></p> <p>The <a href="https://osf.io/e81xl/wiki/home/" rel="nofollow">Reproducibility Project: Cancer Biology</a> has partnered with DDC Medical for STR profiling and mycoplasma testing of all cell lines used in the RP:CB. - We will arrange to send STR and mycoplasma test kits (and rodent pathogen if applicable) to your facility. - You must email the bar codes for each kit to the Project Manager, as this is the only way to track the results. - Return the kits directly to DDC using the provided envelope. - The results will be shared with Science Exchange, and the Project Manager will relay them to you. - Do <em>not</em> begin experimental work until the STR profiling results are confirmed, in case the cells are not the correct line or are contaminated.</p> <p><strong>Protocols that require variance calculations</strong></p> <p>For some protocols, the original data were qualitative in nature (ex; western blots). Thus, our calculations regarding number of replicates were only preliminary. We will highlight these protocols in our initial teleconference before experimental work begins. - Save all materials for this or generated during this experiment (ex; lysates). - Share the results of the replication experiment immediately with the Project Manager. - We will use the replication data to confirm our sample size calculations. - We may need to request additional replicates be run. </p> <p><strong>Data collection</strong></p> <p>All of the data will be uploaded to the Open Science Framework (OSF) as a supplement to the Final Report. We would like to include as many raw files as are available including laboratory notes where necessary. Any file type can be uploaded. - Creating an account on the Open Science Framework - Please view this <a href="https://osf.io/a5imq/wiki/How%20to%20Upload%20Data%20to%20the%20OSF/" rel="nofollow">link</a> for information about setting up an account and uploading data. Or download it as a file; <a href="https://osf.io/9si6v/" rel="nofollow">https://osf.io/9si6v/</a>. This will also share how to upload files to the OSF. - Reporting guidelines: - Many fields have begun instituting guidelines for complete reporting of experimental details. Please see <a href="https://osf.io/a5imq/wiki/Technique%20Specific%20Guidelines%20for%20Reporting/" rel="nofollow">here</a> for details. - Note any deviations from the accepted protocol, including reagents used. - Where possible, within reason, record the lot number of the reagent used (such as inhibitors, growth factors, etc) so additional manufacturer information can be obtained. - All images must be of publication quality and resolution. - At least 300 dpi.</p> <h2>Specific cases:</h2> <p><strong>Western Blots</strong> - Image the full gel, including indicating ladder markers. - Please note which ladder you use so we know what the size markers indicate - Take multiple exposures (ex; 1 sec, 5 sec, 15, sec, 1 min) We will be quantifying western blots, so the data need to be in the linear range. - All images returned must be of high enough quality for publication and analysis (at least 300 dpi).</p> <p><strong>Mouse Health Records and Monitoring</strong> - Date of birth and gender - Breeding records - include genotyping information, such as agarose gels of PCR products - Dates of treatment - Reasons for exclusion, if excluded - Any off-protocol treatments (for example, for a sick mouse) - whether this treatment excludes the animal from analysis</p>
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