Code and Raw Data for Acromegaly and Cushing Analyses

This repository contains raw data for studies done by the Bridges Lab and our collaborators on the neuroendocrine disorders Cushing’s disease and Acromegaly. This repository contains the data for several manuscripts as detailed below. The tag column indicates the state of the dataset at the indicated time.:

Publication	Dataset	Tag
Hochberg, I, I. Harvey, Q. T. Tran, E. J. Stephenson, A. L. Barkan, A. Saltiel, W. F. Chandler, D. Bridges. Gene expression changes in subcutaneous adipose tissue due to Cushing’s disease. Journal of Molecular Endocrinology. 55(2):81-94 (2015). doi:10.1530/JME-15-0119.		Cushing-v1.0.0
Hochberg, I, Q. T. Tran, A. L. Barkan, A. R. Saltiel, W. F. Chandler, D. Bridges. Gene Expression Signature in Adipose Tissue of Acromegaly Patients, PLoS One 10, e0129359 (2015). doi:10.1371/journal.pone.0129359		Acromegaly-v1.0.0
Harvey, I., E. J. Stephenson, J. R. Redd, Q. T. Tran, I. Hochberg, N. Qi, D. Bridges. Glucocorticoid-Induced Metabolic Disturbances Are Exacerbated in Obese Male Mice, Endocrinology 159(6):1-15 (2018). doi:10.1210/en.2018-00147		Obesity-v1.0.0
Gunder, L.C. I. Harvey, J. R. Redd, C. S. Davis, A. AL-Tamimi, S. V. Brooks and D. Bridges. Obesity Augments Glucocorticoid-Dependent Muscle Atrophy in Male C57BL/6J Mice, Biomedicines 2020, 8(10), 420. doi:10.3390/biomedicines8100420		Muscle-v1.0.0

RNAseq data was analysed at first on the mbni and felix servers to generate counts tables. The rest of the analysis was performed locally once the counts table was generated. See the processing folder for the code used in the generation of these alignments and counts tables.

Licence

This CushingAcromegalyStudy data is made available under the Open Data Commons Attribution License: http://opendatacommons.org/licenses/by/1.0. For more information see LICENSE

Data Files

Data files are located in the data directory The raw data in this analysis is located in data/raw.

Script Files

Script files are saved in scripts folder and were analysed via RMarkdown files to generate statistics and plots.

Figures

The figures generated for the manuscript, via the running of these scripts are in the figures directory. These figures are modified for final publication in the manuscript folder using Adobe Illustrator CS6.

Manuscript

The manuscript files, including the manuscript, the figures, tables and supplementary data are in the manuscript directory. Within this directory are the files generated for uploading the raw and processed data to the Gene Expression omnibus (in the folder manuscript/GEO_submission).