Find research datasets worth reusing

opencc-by-4.0Jan 2024View details →

Single-cell RNA-seq profiles of lung adenocarcinoma patients and tumor-bearing mice

single-cell RNA sequencing (scRNA-seq) profiles from eight patients with lung adenocarcinoma (LUAD) and four samples of tumor tissues from tumor bearing mice were performed. By integrating other scRNA-seq data and clinical information, we identified activated adaptive immune responses in older patients, reflected by enriched dysfunctional T cell signature scores and immune checkpoint molecules. Our study shows increased efficacy of immune checkpoint blockade therapy in older patients, addressing the prominent role of age when considering immunotherapy.

opencc-zeroMar 2024View details →

Data from: Repeated sensitization of mice with microfilariae of Litomosoides sigmodontis induces pulmonary eosinophilia in an IL-33-dependent manner

Background: Eosinophilia is a hallmark of helminth infections and eosinophils are essential in the protective immune responses against helminths. Nevertheless, the distinct role of eosinophils during parasitic filarial infection, allergy and autoimmune disease-driven pathology is still not sufficiently understood. In this study, we established a mouse model for microfilariae-induced eosinophilic lung disease (ELD), a manifestation caused by eosinophil hyper-responsiveness within the lung. Methods: Wild-type (WT) BALB/c mice were sensitized with dead microfilariae (MF) of the rodent filarial nematode Litomosoides sigmodontis three times at weekly intervals and subsequently challenged with viable MF to induce ELD. The resulting immune response was compared to non-sensitized WT mice as well as sensitized eosinophil-deficient dblGATA mice using flow cytometry, lung histology and ELISA. Additionally, the impact of IL-33 signaling on ELD development was investigated using the IL-33 antagonist HpARI2. Results: ELD-induced WT mice displayed an increased type 2 immune response in the lung with increased frequencies of eosinophils, alternatively activated macrophages and group 2 innate lymphoid cells, as well as higher peripheral blood IgE, IL-5 and IL-33 levels in comparison to mice challenged only with viable MF or PBS. ELD mice had an increased MF retention in lung tissue, which was in line with an enhanced MF clearance from peripheral blood. Using eosinophil-deficient dblGATA mice we demonstrate that eosinophils are essentially involved in driving the type 2 immune response and retention of MF in the lung of ELD mice. Furthermore, we demonstrate that IL-33 drives eosinophil activation in vitro and inhibition of IL-33 signaling during ELD induction reduces pulmonary type 2 immune responses, eosinophil activation and alleviates lung lacunarity. In conclusion, we demonstrate that IL-33 signaling is essentially involved in MF-induced ELD development.

RNA sequencing of macrophages co-cultured with MSCs and RNA sequencing of alveolar macrophages from mice with lung injury treated with MSCs

RNA sequencing of macrophages co-cultured with MSCS Table 5 RNA sequencing of alveolar macrophages from mice with lung injury treated with MSCS Table 8

Data and ARRIVE 2.0 checklist for the original article "Lockbox enrichment facilitates manipulative and cognitive activities for mice"

This repository contains data (XLSX file) related to the original article "Lockbox enrichment facilitates manipulative and cognitive activities for mice", which was submitted for publication to Open Research Europe. Moreover, the ARRIVE checklist including the ARRIVE Essential 10 and the Recommended Set is provided in Version v2.

Transcriptomic atlas reveals organ-specific disease tolerance in sickle cell mice. Dataset for bone marrow, HbSS Townes mice injected or not with heme

The objective of this experiment was to explore the transcriptome of the HbSS Townes mouse model of sickle cell disease. Townes model mice carry several human hemoglobin knock-in genes replacing the endogenous mouse genes and may be useful in studying sickle cell disease. All mice were genotyped, age- and sex-matched littermates. All HbAA (control, normal human hemoglobin) vs HbSS (sickle cell disease, mutated human hemoglobin) mice were used for experimentations at 6-8 weeks of age, to limit intra-group heterogeneity. Hemin (Ferriprotoporphyrin IX) was purchased from Frontiers Scientific and injected intravenously (iv.) in a retroorbital sinus at a concentration of 24 µmol/kg. Control mice received PBS instead. Mice were anesthetized with isoflurane 2-3% for injections, blood collection and sacrifice. All mice were sacrificed by cervical dislocation, 4 hours after injection. Here the dataset for HbSS mice injected or not with heme is uploaded. The corresponding dataset for the HbAA mice injected or not with heme can be found at 10.5281/zenodo.10961162 Bone marrow RNA was extracted by Macherey Nagel kit, according to the manufacturer’s instructions. The quality and quantity of mRNA were evaluated using a 2100 bioanalyzer with TNA 6000 NanoKits (all Agilent Technologies, Palo Alto, CA, USA). RNA Integrity Numbers superior to 7 were eligible for subsequent reverse transcription into cDNA. RNAseq was performed at the GenomIC plateform Cochin Institute INSERM U1016. After RNA extraction, RNA quality (RNA integrity number) was estimated. 1μg of high-quality total RNA sample (RIN &gt;7) was processed to build up the libraries, using TruSeq Stranded mRNA kit (Illumina) according to manufacturer instructions. Briefly, purified poly-A containing mRNA molecules were fragmented and reverse-transcribed using random primers. Replacement of dTTP by dUTP during second strand synthesis allowed us to achieve strand specificity. Addition of a single A base to the cDNA was followed by ligation of Illumina adapters. Libraries were quantified by qPCR using KAPA Library Quantification Kits for Illumina Libraries (KapaBiosystems, Wilmington, MA). Library profiles were assessed using DNA High Sensitivity LabChip kits on an Agilent Bioanalyzer. Libraries were sequenced on an Illumina Nextseq 500 instrument using 75 base-lengths read V2 chemistry in a paired-end mode. After sequencing, primary analysis based on AOZAN software (ENS, Paris), was applied to demultiplex and control the quality of the raw data (based of FastQC modules / version 0.11.5). The dataset here represents 4 groups of mice, 4 mice per group as follows: HbAA PBS, HbAA heme, HbSS PBS, HbSS heme.

Alpha-synuclein overexpression can drive microbiome dysbiosis in mice

Growing evidence indicates that persons living with Parkinson disease (PD), have a unique composition of indigenous gut microbes. Given the long prodromal or pre-diagnosed period, longitudinal studies of the human and rodent gut microbiome prior to symptomatic onset and for the duration of the disease period are currently lacking. PD is characterized in part by accumulation of the protein α-synuclein (α-syn) into insoluble aggregates, in both the central and enteric nervous systems. As such, a number of experimental rodent and non-human primate models of α-syn overexpression recapitulate some of hallmark pathophysiologies of PD. These animal models provide an opportunity to assess how the gut microbiome changes with age under disease relevant conditions. Here, we used a transgenic mouse strain, the Thy1-hSYN “line 61” mice which over express wild-type human α-syn to test how the gut microbiome composition responds in this model of PD pathology during aging. Using shotgun metagenomics, we find significant, age and genotype dependent bacterial taxa that become altered over age. We reveal that α-syn overexpression can drive alterations to the gut microbiome composition and suggest that it limits the expansion of diversity through age. Given emerging data on potential contributions of the gut microbiome to PD pathologies, our data provide an experimental foundation to understand how the PD-associated microbiome may arise as a trigger or co-pathology to disease.

opencc-zeroFeb 2024View details →

Genetically identical mice express alternative reproductive tactics depending on social conditions in the field

In many species, establishing and maintaining a territory is critical to survival and reproduction, and an animal's ability to do so is strongly influenced by the presence and density of competitors. Here we manipulate social conditions to study the alternative reproductive tactics displayed by genetically identical, age-matched laboratory mice competing for territories under ecologically realistic social environmental conditions. We introduced adult males and females of the laboratory mouse strain (C57BL/6J) into a large, outdoor field enclosure containing defendable resource zones under one of two social conditions. We first created a low-density social environment, such that the number of available territories exceeded the number of males. After males established stable territories, we introduced a pulse of intruder males and observed the resulting defensive and invasive tactics employed. In response to this change in social environment, males with large territories invested more in patrolling but were less effective at excluding intruder males as compared to males with small territories. Intruding males failed to establish territories and displayed an alternative tactic featuring greater exploration as compared to genetically identical territorial males. Alternative tactics did not lead to equal reproductive success—males that acquired territories experienced greater survival and had greater access to females.

opencc-zeroApr 2024View details →

Data from: Non-invasive estimation of absorbed ionizing radiation dose in mice using Near-Infrared Spectroscopy (NIRS) and aquaphotomics

Accurate measurement of ionizing radiation exposure, whether therapeutic or accidental, is of utmost importance in various scenarios. This paper presents a study that addresses this critical need by utilizing near-infrared (NIR) spectroscopy and aquaphotomics to estimate radiation dose exposure in mouse models subjected to X-ray irradiation. The analysis of NIR spectra acquired from the mouse abdomen enabled non-invasive estimation of radiation doses ranging from 0.5 to 6.5 Gy, immediately following the irradiation exposure. The findings were consistent with the impact of total body irradiation in mice, as evidenced by measures such as animal survival rate, alterations in body weight observed over a 30-day post-exposure period, and changes in hematocrit levels. The spectroscopic measurements were based on detecting changes in the molecular structure of body water after radiation exposure, utilizing the water spectral pattern as a multidimensional biomarker. While further validation in nonhuman primates is necessary, the findings demonstrate a simple, non-destructive, and rapid method that holds promise for the estimation of radiation exposure across a range of doses, applicable to both clinical applications and catastrophic radiation events. These advancements in radiation dose quantification have significant implications for the timely and precise assessment of radiation exposure in humans.

opencc-by-4.0Dec 2021View details →

evaluation data for "Capturing the songs of mice with an improved detection and classification method for ultrasonic vocalizations (BootSnap)"

Data contains sound files of mouse vocalization needed to reproduce the evaluation results for "Capturing the songs of mice with an improved detection and classification method for ultrasonic vocalizations (BootSnap)" If you use any of this data, cite the original source: <a href="https://doi.org/10.1016/j.anbehav.2020.09.006">https://doi.org/10.1016/j.anbehav.2020.09.006</a>

opencc-by-4.0Jan 2022View details →

LMT database 2 Shank2-KO & 2 Shank2-WT mice exp 3195

LMT database 2 Shank2-KO & 2 Shank2-WT mice exp 3195 - processed

opencc-by-4.0Feb 2022View details →

Obesity reshapes the microbial population structure along the gut-liver-lung axis in mice

Data repository for the paper: Galaris A., Fanidis D. et al. Obesity reshapes the microbial population structure along the gut-liver-lung axis in mice. 2021 For further data requests and questions please contact the corresponding author of the respective publication. All fastq files have been processed to remove human and mouse sequences.

Data for the paper "Determining the value of preferred goods based on consumer demand in a home-cage based test for mice"

All data related to the paper "Determining the value of preferred goods based on consumer demand in a home-cage based test for mice" will be made available to the scientific public here. The paper will be published soon in Behavioral Research Methods.

A robust method for the measurement of social reward in adult mice

Dataset contains four files. File 1. Harda_et_al._2022_all_data.xlsx All data used in the publication. Results of the social conditioned place preference test perofmed on adult female laboratory mice (strain: C57BL/6). File 2. Harda_et_al._2022_initial_pref_30_70%.xls All data contained in File 1, except for animals that showed initial preference for any of the contexts exceeding 70%. File 3. Harda_et_al._2022_initial_pref_30_70%_trimmed.xlsx Data contained in File 2, randomly trimmed to the same number of animals for each social context. Trimming was performed separately for each experimental group. Data were trimmed by custom R script (File 4). File 4. trimmer.R R script used to randomly trimm data to the same number of animals for each social context.

Data_Figure1(A-D)_AKR1D1 knockout mice develop a sex dependent metabolic phenotype

Data of Fig1 Pannel A-D, “AKR1D1 knockout mice develop a sex dependent metabolic phenotype” The Dataset contains the original figure 1 (Pannel A-D) as PNG-format (10.1530JOE-21-0280_Fig1A-D.PNG). Corresponding raw from LC-MS/MS measurements are provided as one file in CSV format (31003A-179400_10.1530_JOE-21-0280_AKR1D1_SS_DVK_4_Fig1.csv), all further experiment related information (meta-data) as one file in TXT format (31003A-179400_10.1530_JOE-21-0280_AKR1D1_SS_DVK_4_Fig1_M1.txt), one file in PDF format (31003A-179400_10.1530_JOE-21-0280_AKR1D1_SS_DVK_4_Fig1_M2.pdf) and one file as CSV format (31003A-179400_10.1530_JOE-21-0280_AKR1D1_SS_DVK_4_Fig1_M3.csv).

Longitudinal structural MRI, MRS, and behavioral data for mice prenatally exposed to maternal immune activation at gestational day 9

Previous evidence from our lab (https://cobralab.ca/) and others suggest that prenatal exposure to maternal immune activation (MIA) can impact trajectories of neurodevelopment as measured through brain anatomy and behavior in mice. Yet, there are still open questions regarding the alterations to developmental trajectories, as well as the impact on brain chemistry, that this data set seeks to explore. The dataset presented here includes magnetic resonance imaging (MRI) and magnetic resonance spectroscopy (MRS) data from two timepoints, adolescence (postnatal day [PND 35]) and young adulthood (PND 60) in C57BL/6J mice prenatally exposed either to poly I:C (POL) inducing maternal immune activation (MIA) or saline (SAL) at gestational day (GD) 9. The dataset also includes three behaviors acquired after each scanning session with 2 days of rest between the scans and each behavior: open field test, social novel object preference test, and prepule inhibition. Finally, the data also include cytokine assays acquired from a separate sample of pregnant mice and a test-retest of MRS acquired from a voxel in the anterior cingulate area.  The data here published were collected and analyzed for a paper under review, available as a preprint where more details can be found here: https://www.preprints.org/manuscript/202203.0136/v1. In brief, using whole-brain, voxelwise analysis techniques (deformation-based morphometry) we found MIA subtly altered developmental trajectories, reducing volume relative to SAL offspring in the hippocampus and the anterior, right caudate putamen, and increasing volume in the posterior, left caudate putamen and cerebellum. Additionally, there was a trending decrease of myo-inositol and GABA in MIA offspring at PND 60 compared to SAL controls. Finally, there was a trending decrease in ratio of distance travelled in the anxiogenic center zone of an open field compared to the outer areas at PND 35 for MIA offspring.  In this dataset you will find a total of 80 preprocessed structural MRIs in minc format acquired at postnatal day ~35 and ~60 in mice exposed to 5mg/kg poly I:C or vehicle control (0.9% sterile saline) at GD9. The images are included in CUPO_MIA_mncs.zip. These are T1-weighted structural images with two averages; repetition time (TR)/echo time (TE) = 21.55 ms/5.13 ms, matrix size = 260 x 158 x 210, voxel dimensions =&thinsp;70 µm isotropic, flip angle =&thinsp;20°, 23 min total using 5% isoflurane for induction, 1.5% for maintenance of anesthesia during the scan on a cryogenically-cooled surface coil. T1-weighted scans were preprocessed by stripping native coordinates, flipping left-right to maintain fidelity, denoising, correcting inhomogeneities in the bias field using the N4 algorithm, and registering in LSQ6 alignment (i.e. 6 degrees of freedom are allowed for imagine alignment: translations and rotations along x, y, and z dimensions). The demographics information for each animal is included in the demographics.csv file.  Behavioural tests were performed following the postnatal day 35 and 60 scans in all animals with a 2 day rest period. These include: open field test, three chambered social approach, and prepulse inhibition. The data for all of these tests is presented in individual .csv spreadsheet and includes data for both the timepoints evaluated. Additionally, cytokine panels were collected from an independent cohort of 7 dams. MRS data are included in two formats: 1) preprocessed quantifications from LCModel software in csvs, and 2) raw data with press and press_w (respectively water supressed and unsupressed acquisitions) for analysis. The raw data were released in upload version 1.1.0. MRS was acquired from a 1.2 x 2.6 x 2.5 mm3 voxel in the ACA with a Point Resolved Spectroscopy sequence (PRESS; TR/TE=3000/8.5 ms, 256 averages). Within the raw_data.zip, Included in this data set are the structural MRIs in MINC format, the behavioural .csv data, the MRS data (csvs and raw files), and a README file providing further detail on the data structure and content, and on how to interpret the data column titles. DICOMS are also available for the structural MRI data, as are the raw (not-preprocessed) MINC files, available upon request to the authors.

opencc-by-4.0Apr 2022View details →

Protein preference data for male and female mice

These data are from experiments studying protein preference and plasma FGF21 levels in protein-restricted male and female mice conducted at UiT the Arctic University of Norway. These findings will be published Volcko & McCutcheon (2022) bioRxiv. Detailed methods for the experiment can be found in this paper. Full citation to a peer-reviewed publication is expected to follow. Briefly, data are from sessions licking different solutions (casein and/or maltodextrin) in operant chambers, recorded on Med Associates hardware. Accompanying analysis code as a Jupyter notebook is available on Github (https://github.com/mccutcheonlab/ARP).  The data are provided as a compressed zip file containing the following: <ul> <li>Folder with raw datafiles from sessions with a single bottle of either casein or maltodextrin, and two-bottle choice tests</li> <li>Excel file with metadata to accompany each raw datafile (ARP3 and ARP5 conditioning and preference metafile.xls)</li> </ul> The raw datafiles are Med Associates files in the stripped format. ARP3 and ARP5 conditioning and preference metafile.xls contains sheets (metafile_exp1 and metafile_exp2) with the following information for each datafile: <ul> <li>filename</li> <li>mouse ID</li> <li>date</li> <li>diet group (NR, non-restricted or PR, protein-restricted)</li> <li>sex</li> <li>cycle stage (for females in the preference test)</li> <li>nutrient in the left bottle</li> <li>nutrient in the right bottle</li> <li>flavor of the solution in the left bottle</li> <li>flavor of the solution in the right bottle</li> <li>number of licks to the left bottle</li> <li>number of licks to the right bottle</li> <li>phase of the experiment (conditioning sessions or preference test)</li> </ul> ARP3 and ARP5 conditioning and preference metafile.xls also contains sheets (food_intake, BW, female_cycle and FGF21) with data from food intake measurements, body weight measurements, change in food intake and body weight over two cycle in female mice, and plasma FGF21 levels.

opencc-zeroApr 2022View details →

Once an optimist, always an optimist? Studying cognitive judgment bias in mice

This repository contains raw data and analysis code for the manuscript entitled "Once an Optimist, Always an Optimist? Studying Cognitive Judgment Bias in Mice" from Marko Bračić, Lena Bohn, Viktoria Siewert, Vanessa von Kortzfleisch, Holger Schielzeth, Sylvia Kaiser, Norbert Sachser, S. Helene Richter, accepted for publication in the journal Behavioral Ecology. The aim of the study was to investigate the causes and stability of cognitive judgment bias (aka "optimism"). Individuals differ in the way they judge ambiguous information: some individuals interpret ambiguous information in a more optimistic, and others in a more pessimistic way. Over the past two decades, such "optimistic" and "pessimistic" cognitive judgement biases (CJBs) have been utilized in animal welfare science as indicators of animals' emotional states. However, empirical studies on their ecological and evolutionary relevance are still lacking. We, therefore, aimed at transferring the concept of "optimism" and "pessimism" to behavioral ecology and investigated the role of genetic and environmental factors in modulating CJB in mice, using an automated, touchscreen-based active choice paradigm. In addition, we assessed the temporal stability of individual differences in CJB. We show that the chosen genotypes (C57BL/6J and B6D2F1N) and environments ("scarce" and "complex") did not have a statistically significant influence on the responses in the CJB test. By contrast, they influenced anxiety-like behavior (assessed in the elevated plus maze (EPM), an open field test (OFT), and a free exploration test (FET)) with C57BL/6J mice and mice from the "complex" environment displaying less anxiety-like behavior than B6D2F1N mice and mice from the "scarce" environment. As the selected genotypes and environments did not explain the existing differences in CJB, future studies might investigate the impact of other genotypes and environmental conditions on CJB, and additionally, elucidate the role of other potential causes like endocrine profiles and epigenetic modifications. Furthermore, we show that individual differences in CJB were repeatable over a period of seven weeks, suggesting that CJB represents a temporally stable trait in laboratory mice. Therefore, we encourage the further study of CJB within an animal personality framework.

opencc-by-4.0Jun 2022View details →

Prosocial behavior in adult mice is sex-dependent

The data from three behavioral test performed on adult male and female C57BL/6 mice. 1_Misiolek_et_al_2022_Prosocial.csv Two-choice food motivated prosocial behavior task. 2_Misiolek_et_al_2022_SCPP.csv Social conditioned place preference test. 3_Misiolek_et_al_2022_Affective_State_Discriminatiion.csv Affective State Discrimination test.

opencc-by-4.0Aug 2022View details →

Time to run: Late rather than early exercise training in mice promotes fat mass loss and reduces atherosclerosis development

This dataset contains forward and reverse reads of 16S sequencing of the V3-V4 region of caecal bacteria. As indicated in the metadata file, mice are divided into three groups - SED (sedentary mice, E-SED for early sedentary and L-SED for late sedentary), E-RUN (early runners) and L-RUN (late runners). For more information about the groups, sequencing etc., consult the manuscript.