DOI: 10.5061/dryad.1rn8pk11r
title: Pleiotropic effects of trisomy and pharmacologic modulation on structural, functional, molecular, and genetic systems in a Down syndrome mouse model

description: Down syndrome (DS) is characterized by skeletal and brain structural
 malformations, cognitive impairment, altered hippocampal metabolite
 concentration, and gene expression imbalance. These alterations were
 usually investigated separately, and the potential rescuing effects of
 green tea extracts enriched in epigallocatechin-3-gallate (GTE-EGCG)
 provided disparate results due to different experimental conditions. Since
 a holistic evaluation of these systems is missing, we designed a
 longitudinal experimental setup to follow the simultaneous development of
 structural, functional, molecular, and genetic alterations in the Ts65Dn
 mouse model. In this study, we conducted a multi-modal in vivo imaging
 study using microcomputed tomography (µCT), magnetic resonance imaging
 (MRI), and magnetic resonance spectroscopy (MRS) to investigate the
 integrated development of craniofacial shape, BMD, brain volumes, and
 hippocampal metabolites in wildtype and Ts65Dn mice. Additionally, we
 evaluated the changes in body weight and performed a battery of
 neurodevelopmental and adult cognitive tests to assess cognitive function
 from birth to adulthood throughout development. At the endpoint, we also
 evaluated tibia microarchitecture from ex vivo µCT scans and used
 RNAseq to analyze cerebellar gene expression in the same mice at eight
 months old.
description: # Pleiotropic effects of trisomy and pharmacologic modulation on
 structural, functional, molecular, and genetic systems in a Down syndrome
 mouse model
 [https://doi.org/10.5061/dryad.1rn8pk11r](https://doi.org/10.5061/dryad.1rn8pk11r) The dataset contains the results of adult cognitive testing, body weight, bone mineral density, concentration of brain hippocampal metabolites, brain volumes, frequency of maternal behavior, neurodevelopmental testing, RNAseq counts, skull shape landmarking files and tibia microarchitecture readouts at different developmental stages for wild-type untreated mice (WT), Ts65Dn untreated mice (TS), wild-type mice treated with GTE-EGCG (WT TREATED) and Ts65Dn mice treated with GTE-EGCG (TS TREATED). ## **Description of the data and file structure** *Adult cognitive testing:* Results from Open Field (OF), Elevated Plus Maze (EPM), Sociability/Preference for Social Novelty (SPSN), Novel Object Recognition (NOR) and Passive Avoidance (PA) tests. The first sheet contains the results at timepoint Cog.1, and the second sheet contains the results at timepoint Cog.2, as defined in the experimental setup. Note that even though the treatment was stopped after Cog.1, the groups at Cog.2 are still named 'Treated' for identification purposes. Missing values are denoted by NA. * For PA, the latency to enter the dark chamber before presentation of the stimuli is shown in column C and the latency to enter the dark chamber after presentation of the stimuli is shown in column D, expressed in seconds. * For EPM, the percentage of time spent in the open arm is shown in column E. * For OF, the total distance covered by each mouse is shown in column F, expressed in meters; the mean speed of each mouse is shown in column G, expressed in m/sec; the time spent in the periphery is shown in column H, expressed in seconds; and the time spent in the center is shown in column I, expressed in seconds. * For NOR, the total distance covered by each mouse during the habituation phase of the test is shown in column J, expressed in meters; the mean speed of each mouse during the habituation phase of the test is shown in column K, expressed in m/sec; the time spent in the center during the habituation phase of the test is shown in column L, expressed in seconds; and the preference for the novel object is shown in column M, expressed as a percentage. * For SPSN, the total distance covered by each mouse during the habituation phase of the test is shown in column N, expressed in meters; the mean speed of each mouse during the habituation phase of the test is shown in column O, expressed in m/sec; and the preference for the novel stranger mouse is shown in column P, expressed as a percentage. *Body weight:* Each sheet contains the body weight measurements expressed in grams for a different timepoint. The first sheet contains the body weight of each mouse from developmental day 1 to developmental day 17 (columns C to S). The second sheet contains the body weight of each mouse at timepoint BW2 (column C), and the third sheet contains the body weight of each mouse at timepoint BW3 (column C), as defined in the experimental setup. Note that even though the treatment was stopped after BW2, the groups at BW3 are still named 'Treated' for identification purposes. Missing values are denoted by NA. *Bone mineral density:* Bone mineral density (BMD) of the humerus estimated from *in vivo* µCT scans reported in mgHAp/cm^3 at different timepoints. Column C contains the BMD measured at µCT1, column D contains the BMD measured at µCT2, column E contains the BMD measured at µCT3, and column F contains the BMD measured at µCT4, as defined in the experimental setup. Note that even though the treatment was stopped after µCT3, the groups at µCT4 are still named 'Treated' for identification purposes. Missing values are denoted by NA. *Brain hippocampal metabolites:* The file 'Metabolite quantification' contains the concentration of N-acetylaspartate (NAA, column C), creatine + phosphocreatine (Cr+PCr, column D), choline + phosphocholine + glycerophosphocoline (tCho, column E), myo-inositol (myo-Inos, column F) and taurine (Tau, column G) estimated from *in vivo* MRS performed in the hippocampal region, reported in mmol/kg. The file 'Spectral region quantification' contains the relative integrals of 12 spectral regions between 0.0 ppm and 4.3 ppm estimated from *in vivo* MRS performed in the hippocampal region (columns C to N). The main metabolites present in each spectral region are listed in the sheet named 'Spectral region information'. In both files, the first sheet contains the results at time point MRS1 and the second sheet contains the results at time point MRS2, as defined in the experimental setup. Note that even though the treatment was stopped after MRS1, the groups at MRS2 are still named 'Treated' for identification purposes. Missing values are denoted by NA. *Brain volume:* The body weight of each mouse is shown in column C, expressed in grams; the number of voxels of the whole brain, hippocampal region, cerebellum, lateral ventricles, third ventricle, fourth ventricle, cerebral aqueduct, and whole ventricular system estimated from *in vivo* MRI are shown in columns D to K; the number of voxels of the whole brain, hippocampal region, cerebellum, lateral ventricles, third ventricle, fourth ventricle, cerebral aqueduct, and whole ventricular system estimated from *in vivo* MRI normalized to the body weight of each mouse are shown in columns L to S; the volumes of the whole brain, hippocampal region, cerebellum, lateral ventricles, third ventricle, fourth ventricle, cerebral aqueduct, and whole ventricular system estimated from *in vivo* MRI are shown in columns T to AA, expressed in mm^3; and the volumes of the whole brain, hippocampal region, cerebellum, lateral ventricles, third ventricle, fourth ventricle, cerebral aqueduct, and whole ventricular system estimated from *in vivo* MRI normalized to the body weight of each mouse are shown in columns AB to AI. The first sheet contains the results at timepoint MRI1 and the second sheet contains the results at timepoint MRI2, as defined in the experimental setup. Note that even though the treatment was stopped after MRI1, the groups at MRI2 are still named 'Treated' for identification purposes. *Maternal care:* The frequency of nursing (row 2), pup licking (row 3), digging in nest (row 4), eating (row 5), drinking (row 6), moving (row 7) and digging off nest (row 8) for the Ts65Dn pregnant mothers are shown in each row, presented as number of times the mother showed each behavior. Frequencies during daytime are presented in the first sheet and frequencies during nighttime are presented in the second sheet. Data for untreated mothers are presented on columns B to G and data for treated mothers are presented in columns H to N. *Neurodevelopmental testing:* The file 'Acquisition rate' contains the results for the eye opening test (first sheet, 0 indicates absence of eye opening, 1 indicates presence), the pinna detachment test (second sheet, 0 indicates absence of pinna detachment, 1 indicates presence), the walking test (third sheet, 0 indicates absence of walking, 1 indicates presence), the cliff drop aversion test (fourth sheet, 0 indicates absence of the reflex, 1 indicates presence), the Preyer reflex test (fifth sheet, 0 indicates absence of the reflex, 1 indicates presence), the blast response (sixth sheet, 0 indicates absence of the reflex, 1 indicates presence), the visual placing test (seventh sheet, 0 indicates absence of visual placing, 1 indicates presence), the reaching response test (eighth sheet, 0 indicates absence of response, 1 indicates presence), the vibrissae placing test (nineth sheet, 0 indicates absence of vibrissae placing, 1 indicates presence), the tactile response test (tenth sheet, 0 indicates absence of response, 1 indicates presence), the incisor eruption test (eleventh sheet, numbers indicate the score obtained by each mouse), the surface righting response test (twelfth sheet, numbers indicate the score obtained by each mouse), the negative geotaxis test (thirteenth sheet, numbers indicate the score obtained by each mouse), the vertical climbing test (fourteenth sheet, numbers indicate the score obtained by each mouse), the grasping test (fifteenth sheet, numbers indicate the score obtained by each mouse), the homing test (sixteenth sheet, results shown as seconds), and the pivoting test (seventeenth sheet, results shown as degrees pivoted by each mouse). In each sheet, each column shows the results for a given postnatal day, indicated in the second row. The file 'Average day of successful test completion' shows the postnatal day at which the eye opening test (column C), the pinna detachment test (column D), the walking test (column E), the cliff drop aversion test (column F), the Preyer reflex test (column G), the blast response (column H), the visual placing test (column I), the reaching response test (column J), the vibrissae placing test (column K), the tactile response test (column L), the incisor eruption test (column M), the surface righting response test (column N), the negative geotaxis test (column O), the vertical climbing test (column P), and the grasping test (column Q) was successfully completed. Missing values are denoted by NA. *RNAseq:* Read counts of each gene (shown in different rows) estimated from RNAseq performed in a cerebellar tissue homogenate for each mouse (shown in columns). Note that even though the treatment had been stopped for three months at the stage where RNAseq was performed, the groups are still named 'Treated' for identification purposes. *Skull shape:* Each folder contains the landmark file for each mouse showing the x,y,z coordinate of each landmark in Ascii format collected manually on the skull segmented from *in vivo* µCT scans at timepoints µCT1 (folder named 'Landmarks uCT1'), µCT2 (folder named 'Landmarks uCT2'), µCT3 (folder named 'Landmarks uCT3'), and µCT4 (folder named 'Landmarks uCT4'), as defined in the file 'Experimental setup'. Each folder contains sub-folders separating the landmark files by experimental group. Note that even though the treatment was stopped after µCT3, the groups at µCT4 are still named 'Treated' for identification purposes. *Tibia microarchitecture:* The percentage of bone volume is shown in column C (BV/TV, expressed as a percentage), the trabecular number is shown in column D (Tb.N, expressed as 1/mm), the trabecular thickness is shown in column E (Tb.Th, expressed as mm), the trabecular separation is shown in column F (Tb.Sp, expressed as mm), the bone mineral density is shown in column G (BMD, expressed as g/cm^3), the cross sectional area is shown in column H (Tt.Ar, expressed as mm^2), the periosteal perimeter is shown in column I (Ps.Pm, expressed as mm), the endosteal perimeter is shown in column J (Ec.Pm, expressed as mm), the bone area is shown in column K (Ct.Ar, expressed as mm^2), the medullary area is shown in column L (Ma.Ar, expressed as mm^2), the cortical thickness is shown in column M (Ct.Th, expressed as mm), the cortical porosity is shown in column N (Ct.Po, expressed as a percentage), the polar moment of inertia is shown in column O (J, expressed as mm^4), the cortical bone mineral density is shown in column P (Ct. BMD, expressed as g/cm^3), and the length of the tibia is shown in column Q (expressed as mm). All values were estimated from an *ex vivo* µCT scan at endpoint. Note that even though the treatment had been stopped for three months at the stage where the *ex vivo* µCT scan was performed, the groups are still named 'Treated' for identification purposes.