<h2><strong>Experimental Guidelines for Replicating Labs</strong></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>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>
- 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
- 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>