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Registered report: transcriptional amplification in tumor cells with elevated c-Myc.

David Blum | Haiping Hao | Michael McCarthy | Reproducibility Project: Cancer Biology
eLife | 2015

The Lin et al. (2012), published in Cell in 2012. The experiments that will be replicated are those reported in Figures 3E and 3F. In these experiments, elevated levels of c-Myc in the P493-6 cell model of Burkitt's lymphoma results in an increase of the total level of RNA using UV/VIS spectrophotometry (Figure 3E; Lin et al., 2012) and on the mRNA levels/cell for a large set of genes using digital gene expression technology (Figure 3F; Lin et al., 2012). The Reproducibility Project: Cancer Biology is a collaboration between the eLife.

Pubmed ID: 25621564

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This is a list of tools and resources that we have found mentioned in this publication.


Center for Open Science (tool)

RRID:SCR_003239

Non-profit organization to increase the openness, integrity, and reproducibility of scientific research. COS priorities are to (1) make the entire scientific workflow accessible, (2) increase scientists' accountability, (3) facilitate good practices by scientists, (4) increase reward for good practices, and (5) promote reproducibility of scientific findings. COS has three primary activities: * Infrastructure development to support the scientific workflow and to connect technologies that support scientific research and communication, such as the Open Science Framework * Community building on open practices among open-source developers, open science researchers, and the broader scientific community, such as the Open Science Collaboration * Metascience, research on scientific practices, such as Reproducibility Project: Psychology and our partnership with Science Exchange, Reproducibility Project: Cancer Biology.

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ScienceExchange (tool)

RRID:SCR_010620

Access service resource which connects labs needing and offering experimental services. Users can search for academic and government labs and experimental services, request and compare service quotes, and directly communicate with labs to arrange orders.

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Novus Biologicals (tool)

RRID:SCR_004286

Commercial antibody vendor which supplies antibodies and other products to life science researchers.

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Image Lab Software (tool)

RRID:SCR_014210

Imaging software used to acquire and analyze images from specific Bio-Rad imaging systems. Users can analyze gel or blot features, capture optimized image data, and generate a report of the data. Image Lab software exclusively runs on the Gel Doc EZ imager, Gel Doc XR+ imaging system, ChemiDo MP, ChemiDoc XRS+ imaging systems, Criterion Stain Free imager, and the GS-900calibrated densitometer.

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c-Myc (N-term) (antibody)

RRID:AB_562270

This monoclonal targets MYC

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Anti-β-Actin Antibody (antibody)

RRID:AB_476744

This monoclonal targets slightly modified β-cytoplasmic actin N-terminal peptide, Ac-Asp-Asp-Asp-Ile-Ala-Ala-Leu-Val-Ile-Asp-Asn-Gly-Ser-Gly-Lys, conjugated to KLH

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nSolver Analysis Software (data processing software)

RRID:SCR_003420

A data analysis software program that offers nCounter users the ability to QC, normalize, and analyze data without having to purchase additional software packages.

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GraphPad Prism (software resource)

RRID:SCR_002798

Statistical analysis software that combines scientific graphing, comprehensive curve fitting (nonlinear regression), understandable statistics, and data organization. Designed for biological research applications in pharmacology, physiology, and other biological fields for data analysis, hypothesis testing, and modeling.

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G*Power (software resource)

RRID:SCR_013726

Data analytics software to compute statistical power analyses for many commonly used statistical tests in social and behavioral research. It can also be used to compute effect sizes and to graphically display the results of power analyses.

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GeneSnap (software resource)

RRID:SCR_014249

A software program used to control G:BOX hardware, specifically to capture and process images. While viewing images in real time, GeneSnap controls the illumination and exposure length of the lens, as well as the focussing, zooming and iris setting of a motorized lens.

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Open Science Framework (storage service resource)

RRID:SCR_003238

Platform to support research and enable collaboration. Used to discover projects, data, materials, and collaborators helpful to your own research.

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