Example AMPA Receptor and Housekeeping Protein Expression Data from Male Long-Evans Rats for the Purpose of Demonstrating the blotRig Western Blot Tool

DOI:10.34945/F51C7B

DATASET CITATION

Omondi C., Chou A., Fond K., Morioka K., Joseph N. R., Sacramento J. A., Iorio E. G., Torres-Espin A., Radabaugh H. L., Davis J. A., Gumbel J. H., Huie J. Russell., Ferguson A. R. (2024) Example AMPA Receptor and Housekeeping Protein Expression Data from Male Long-Evans Rats for the Purpose of Demonstrating the blotRig Western Blot Tool. Open Data Commons for Spinal Cord Injury. ODC-SCI:939 http://doi.org/10.34945/F51C7B

ABSTRACT

STUDY PURPOSE: The purpose of this study is to demonstrate best practices in analyzing western blot data. This study uses example western blot data from a spared peripheral nerve + spinal cord injury model to illustrate how technical replications and counterbalancing of experimental groups across western blot gels can improve rigor and reproducibility. The data are organized to be used easily in the blotRig tool, which we developed to aid in western blot experimental design and analysis.

DATA COLLECTED: The data collected are from 29 male Long-Evans rats that were grouped prior to western blot analysis into one of two groups, and spinal cord tissue was prepared for western blot analysis. Each sample was run on three technical replicate western blot gels, and densitometry values for the target protein (GluA2 AMPA receptor subunit) and beta actin loading controls were collected and analyzed.

CONCLUSIONS: These data were used to demonstrate the varying ways that western blot data can be analyzed. The data included here are organized so that an analyst can easily use these in the blotRig tool, where a linear mixed model is implemented to capture the random effect of replication and loading control as a covariate when assessing whether there are group differences in expression level for a target protein. These data will be forthcoming in an unblinded way, and this dataset will be cross-referenced

KEYWORDS

Western blot; Reproducible Western blot

PROVENANCE / ORIGINATING PUBLICATIONS

RELEVANT LINKS

blotRig Tool

https://github.com/ucsf-ferguson-lab/blotRig/

this is the blotRig analytical tool that can be tested using these example western blot data

NOTES

DATASET INFO

Contact: Huie J (russell.huie@ucsf.edu)

Lab: Ferguson Lab

ODC-SCI Accession:939

Records in Dataset: 87

Fields per Record: 6

Last updated: 2024-02-22

Date published: 2024-02-22

Downloads: 12

Files: 2

LICENSE

Creative Commons Attribution License (CC-BY 4.0)

FUNDING AND ACKNOWLEDGEMENTS

NIH grants R01NS088475 (ARF), R01NS122888 (ARF), UH3NS106899 (ARF), U24NS122732 (ARF), VA grants I01RX002245 (ARF), I01RX002787 (ARF), I50BX005878 (ARF), Wings for Life (ARF) , Craig H. Neilsen Foundation (ARF)

CONTRIBUTORS

Omondi, Cleopa

UCSF

Chou, Austin

UCSF

Fond, Kenneth

UCSF

Morioka, Kazuhito

UCSF

Joseph, Nadine R.

UCSF

Sacramento, Jeffrey A.

UCSF

Iorio, Emma G.

UCSF

Torres-Espin, Abel

UCSF

Radabaugh, Hannah L.

UCSF

Davis, Jacob A.

UCSF

Gumbel, Jason H.

UCSF

Huie, J Russell.

UCSF

Ferguson, Adam R.

UCSF