DOI: 10.5061/dryad.70rxwdc92
title: Data from: Cellular and molecular mechanisms that shape the development and evolution of tail vertebral proportion in mice and jerboas

description: Limbs and vertebrae elongate by endochondral ossification, but local
 growth control is highly modular, such that not all bones are the same
 length. Compared to limbs, which have a different evolutionary and
 developmental origin, far less is known about how individual vertebrae
 establish proportion. Using the jerboa and mouse tail skeletons, we find
 that cell number is a common driver of limb and vertebral proportion in
 both species. However, chondrocyte hypertrophy, which is a major driver of
 proportion in all mammal limbs, is limited to the extreme disproportionate
 growth of jerboa mid-tail vertebrae. The genes associated with
 differential growth in the vertebral skeleton overlap significantly, but
 not substantially, with genes associated with limb proportion. Among
 shared candidates, loss of Natriuretic Peptide Receptor 3 in mice causes
 disproportionate elongation of the proximal and mid-tail vertebrae, in
 addition to the proximal limb. Our findings, therefore, reveal cellular
 processes that tune the growth of individual vertebrae while also
 identifying natriuretic peptide signaling among genetic control mechanisms
 that shape the entire skeleton.
description: # **Cellular and genetic mechanisms that shape the development and
 evolution of tail vertebral proportion in mice and jerboas** Dataset DOI:
 [10.5061/dryad.70rxwdc92](10.5061/dryad.70rxwdc92) ## Description of the
 data and file structure This dataset is associated with the research
 manuscript entitled ‘*Cellular and genetic mechanisms that shape the
 development and evolution of tail vertebral proportion in mice and
 jerboas*’
 ([https://www.biorxiv.org/content/10.1101/754002v2](https://www.biorxiv.org/content/10.1101/2024.10.25.620311v1)). The folder ‘**DRYAD_Weber_etal_2025**’ contains: * Analysis code used for jerboas-mouse differential RNASeq analysis (**Weber_Interspecies_DESEQ2_analysis.R** and **RNAseq_analysis.Rmd**) - Two gtf annotation files for 1:1 and 1:0 orthologs in Mouse (one2one_one2zero_mus_minus_gm49394) and Jerboa (one2one_one2zero_jac_minus_gm49394) genomes generated with TOGA. This folder also contains two files with mouse or jerboa gene lengths in non-overlapping exons of each gene in the 1:1 and 1:0 orthologous GTF annotations (o2o_o2z_mus_exon_length.txt and o2o_o2z_jac_exon_length.txt). A supporting R library required to run the analysis is provided in this folder (weitzel_shared_library.R). * STAR generated GeneCounts for mouse and jerboa samples (suffixed "*_SR50"). Subfolders contain jerboa (Jac_P16) and mouse (Mus_P7) STAR Genecounts used in the analyses. - Raw DESeq2 differential expression results for inter- and intra-species analysis are in the .csv files beginning with "DESeq2_" followed by the comparison leveraged. For example \_CD6 is a differential expression analysis comparing mouse and jerboa CD6, as described in the associated manuscript.  - FASTQ PE reads and FASTQC files samples using the analyses. File naming information is located in fastq_key.xlsx. Briefly, the files are named in the following scheme: SpeciesAge_VertebraEnd_Sample#_xxx_xxxx_R#_xxx.fastq.gz where R# refers to the pair-end read. For example, musP7_cd1cranial_13_S86_L001_R1_001.fastq.gz refers to a cartilage pool from 3 mice age postnatal day 7, tail vertebrae 1 (cd1) cranial end, sample #13, R1 (paired-end 1). Species are either mus (mouse) or jac (jerboa), postnatal day 7 (P7) or day 16 (P16), tail vertebra 1 (cd1) or 6 (cd6) at the cranial end of element. These are also detailed in the fastq_key file.  - Original python program to analyze uCT data written by co-author AJW * NPR3_CTscan.zip are all raw measurements of NPR3 tail vertebral lengths from uCT scans. Compiled_measurement_files folder contains NPR3summarizeddata.csv file of all measurements. The Raw_measurements folder is separated by each individual (labeled as SexID#_Age) where each folder contains pixel intensities across a linear measurement for each vertebra. These folders were fed into the python program to produce vertebral lengths. The outputs from this program are in files output_NPR3_P7 and \_P42  - NPR3_imaging.zip include raw and processed images of NPR3 antibody immunofluorescence and H&E stained vertebra sections. The raw and processed measurements are in file NPR3_GPmeasurements.xlsx and the key (to match image ID with sample identity) is in file NPR3_histologyimage_key.xlsx.  * MusJac_imaging.zip is broken into Mouse and Jerboa folders. Each folder includes all raw measurements of mouse and jerboa tail vertebral lengths from uCT scans, raw and processed immunofluorescent images from EdU and Calcein experiments detailed in the associated manuscript, and H&E stained sections. Each experiment folder is organized by date of experiment and has a collated measurements file that includes a key (to match image ID with sample identity). ## Code/software RStudio – Used for data analysis, visualization, and running R scripts included in the repository. Python 3 – Used for data processing, scripting, or additional analysis tasks, depending on the specific needs of the project.