DOI: 10.4231/6dts-8269
title: Supporting data for "Nanostructural Changes in Bone Quality in a Mouse Model of Chronic Kidney Disease and Treatment with Calcitonin"

description: &lt;p&gt;The purpose of this study was to evaluate the micro- and nano-structural changes in femoral cortical bone in mice impacted by chronic kidney disease (CKD) and undergoing in vivo treatment with synthetic salmon calcitonin. Protocols were approved by the Indiana University Indianapolis School of Science Institutional Animal Use and Care Committee. (&lt;span style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; display: inline !important; float: none;"&gt;Indiana University-Indianapolis School of Science Protocol #SC335R.)&lt;/span&gt;&lt;/p&gt;

&lt;p&gt;This data set supports the publication: Montagnino, E., Bush, W., Bustamante, J., Bandara, W., Jalaie, P., Allen, M.R., Wallace, J.M., Siegmund, T., Surowiec, R.K. and Howarter, J.A., 2025. Nanostructural changes in bone quality in a mouse model of chronic kidney disease and treatment with calcitonin. &lt;i&gt;Bone Reports&lt;/i&gt;, p.101880.&lt;/p&gt;

&lt;p&gt;Analysis of the microstructure was conducted using microCT, yielding values for total area, cortical area, cortical thickness, bone area, and cortical porosity. The nanostructure was evaluated with SAXS and WAXS, whose outcomes report mineral thickness, mineral length, D-periodicity, and collagen lateral spacing. The composition of the bone was analyzed with TgA, reporting values for mineral, collagen, and bound water wt.%. Biochemistries are reported as BUN level and PTH level. For data processing methods, please see the following manuscript in Bone Reports from Montagnino et al., &quot;Nanostructural Changes in Bone Quality in a Mouse Model of Chronic Kidney Disease and Treatment with Calcitonin&quot;.&lt;/p&gt;

&lt;p&gt;SAXS and WAXS nexus file names do not refer to any particular sample group but are overall a description of the project, and each file contains data for multiple samples, where the name is embedded in the nexus file for each sample. There are three nexus files for each round of data collection, as three spots for each sample were collected to be averaged together. SAXS and WAXS data were processed using the Python script located in &lt;span style="font-size:11pt"&gt;&lt;span new="" roman="" style="font-family:" times=""&gt;Bush, W. D.; Montagnino, E. S.; Siegmund, T. H.; Howarter, J. A. (2025), &quot;&lt;a href="https://purr.purdue.edu/publications/4894/1" style="color:blue; text-decoration:underline"&gt;Code for Processing Laboratory SAXS/WAXS Data in NEXUS File Format&lt;/a&gt;.&quot; Purdue University Research Repository (DOI: &lt;a href="https://doi.org/10.4231/A21M-D344" style="color:blue; text-decoration:underline" target="_blank"&gt;10.4231/A21M-D344&lt;/a&gt;).&lt;/span&gt;&lt;/span&gt;&lt;/p&gt;

&lt;p&gt;Along with the raw NEXUS files from the instrument, the processed 1D curves are available in .csv files. The .csv files were used in SASview for fitting the third-order periodicity peak and the Lorentz curves; the corresponding .pdf for each fit is included.&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;** Due to not being able to relabel the sample names embedded in the nexus files, sample #23 was mislabeled as a CKD CAL sample when it is a CKD sample. This mislabeling should be taken into account, and CKD_23 should be included in the CKD untreated values.** &lt;/strong&gt;&lt;/p&gt;

&lt;p&gt;All Analysis Compiled.xlsx : Meta data file includes sample key (For control groups, the samples were labeled as &quot;CON&quot; or &quot;WT_Untreated&quot;. The groups for CKD begin with &quot;CKD&quot; or &quot;CKD_Untreated&quot; and any group treated with calcitonin is denoted with a &quot;CAL&quot;), processed values for MicroCT (total area, cortical area, cortical thickness, bone area, and cortical porosity), biochemistries (BUN level and PTH level), TGA (mineral, collagen, and water wt.% for each sample), SAXS and WAXS (mineral thickness, mineral length, D-periodicity, and collagen lateral spacing).&lt;/p&gt;

&lt;p&gt;TgA Raw Data Compiled.xlsx : Raw TGA data for each sample curve, including temperature vs. weight %. OriginPro was used to take the derivative of each sample&#39;s curve. &lt;/p&gt;

&lt;p&gt;uCT Data Summary.xlsx : Raw MicroCT derived data. &lt;/p&gt;

&lt;p&gt;SWAXS: Directory contains SAXS and WAXS data&lt;/p&gt;

&lt;p&gt;SAXS RAW: Raw data for SAXS in NEXUS file format&lt;/p&gt;

&lt;p&gt;WAXS RAW: Raw data for WAXS in NEXUS file format&lt;/p&gt;

&lt;p&gt;Control Groups_45deg integration: 1D reduced data (intensity vs q) for 45deg integration of SAXS data for Controls (treated and untreated) specimens. csv file format&lt;/p&gt;

&lt;p&gt;Control Groups_360deg integration: 1D reduced data (intensity vs q) for 360deg integration of SAXS data for Controls (treated and untreated) specimens. csv file format&lt;/p&gt;

&lt;p&gt;CKD Groups_45deg integration: 1D reduced data (intensity vs q) for 45deg integration of SAXS data for CKD (treated and untreated) specimens. csv file format&lt;/p&gt;

&lt;p&gt;CKD Groups_360deg integration: 1D reduced data (intensity vs q) for 360deg integration of SAXS data for CKD (treated and untreated) specimens. csv file format&lt;/p&gt;

&lt;p&gt;Lorentzian Fit Files: SASView analysis, file names refer to sample key, pdf format&lt;/p&gt;

&lt;p&gt;Third Order Peak Fit Files: SASView analysis, file names refer to sample key, pdf format&lt;/p&gt;

&lt;p&gt;WAXS (002) peak fits: SASView analysis, Gaussian fits to raw data, file names refer to sample key, txt format&lt;/p&gt;

&lt;p&gt;WAXS 1D integration:1D reduced WAXS data (intensity vs q), file names refer to sample key, csv format&lt;/p&gt;

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description: This data was collected for the manuscript published in Bone Reports, "Nanostructural Changes in Bone Quality in a Mouse Model of Chronic Kidney Disease and Treatment with Calcitonin". The files document biochemistries, microCT data, SAXS/WAXS, and TGA.