## Replication Study: Transcriptional amplification in tumor cells with elevated c-Myc <br> **Abstract:** As part of the [Reproducibility Project: Cancer Biology][1], we published a Registered Report ([Blum et al., 2015][2]), that described how we intended to replicate selected experiments from the paper "Transcriptional amplification in tumor cells with elevated c-Myc" ([Lin et al., 2012][3]). Here we report the results. We found overexpression of c-Myc increased total levels of RNA in P493-6 Burkitt’s lymphoma cells; however, while the effect was in the same direction as the original study (Figure 3E; [Lin et al., 2012][4]), statistical significance and the size of the effect varied between the original study and the two different lots of serum tested in this replication. Digital gene expression analysis for a set of genes was also performed on P493-6 cells before and after c-Myc overexpression. Transcripts from genes that were active before c-Myc induction increased in expression following c-Myc overexpression, similar to the original study (Figure 3F; [Lin et al., 2012][5]). Transcripts from genes that were silent before c-Myc induction also increased in expression following c-Myc overexpression, albeit less than active genes. Treating the data as paired, we found a statistically significant increase in gene expression for both active and silent genes upon c-Myc induction; however, the change in gene expression was found to be greater for active genes compared to silent genes. Finally, we report meta-analyses for each result, which suggests total RNA levels increased upon c-Myc induction, with increased gene expression observed in both active and, to a lesser extent, silent genes. ---------- ### Contents **Reports:** Read the [Replication Study][6] or view the [preprint versions][7]. **Note**: In order to successfully run and knit the Replication Study Manuscript R Markdown file, you must install a series of necessary R packages. You can review the necessary packages included in the checkpoint manifest in the markdown file [here][8] or run and knit the following r markdown file and they will be downloaded automatically. To reproduce the Replication Study manuscript text run this in [R Studio][9] (note: downloads [R markdown file][10] directly from osf.io: library(httr) library(pander) library(rmarkdown) GET("https://osf.io/vdrsh/?action=download",write_disk("Replication_Study_48.Rmd", overwrite = T)) render("Replication_Study_48.Rmd", output_format = "word_document") <br> Also, explore the Registered Report and materials related to the Registered Report [here][11]. **Data and Material Availability:** All associated data, protocols, analysis scripts, and other digital materials are available within this OSF project. **Experiments replicated**: Reproduce and explore the figures, analyses, data, and methods generated in this replication attempt. <br> - [Western blot of c-Myc reactivation in tetracyclic-repressible system and total RNA expression during c-Myc re-activation][12] <br> -Replication of Figures 1B and 3E of Lin et al., 2012 - [Transcript levels during c-Myc re-activation and NanoString nCounter digital gene expression assay][13] <br> -Replication of Figure 3F and Table S1 of Lin et al., 2012 **Meta-analysis**: As a measure of evaluating reproducibility a meta-analysis of each effect was performed. The forest plots, analyses, and data are available [here][14]. <br> Questions about the project can be directed to [contact+rpcb@cos.io.][15] [1]: https://osf.io/e81xl/wiki/home/ [2]: https://elifesciences.org/articles/04024 [3]: http://www.cell.com/cell/fulltext/S0092-8674(12)01057-4 [4]: http://www.cell.com/cell/fulltext/S0092-8674(12)01057-4 [5]: http://www.cell.com/cell/fulltext/S0092-8674(12)01057-4 [6]: https://doi.org/10.7554/eLife.30274 [7]: https://osf.io/n7tqh/ [8]: https://osf.io/vdrsh/ [9]: https://www.rstudio.com [10]: https://osf.io/vdrsh/ [11]: https://elifesciences.org/articles/04024 [12]: https://osf.io/tfd57/wiki/home/ [13]: https://osf.io/fn2y4/wiki/home/ [14]: https://osf.io/5yscz/wiki/home/ [15]: mailto:contact+rpcb@cos.io