RNAseq data for Hassani et al. "Environmental enrichment regulates inter-individual transcriptional variance in the hippocampus"
Description of the data | The Excel table contains in row the different transcripts that were detected. The headers of the first columns are: Geneid Gene_symbol, Chromosome, Start, End, Strand, GeneBiotype,GeneBiotype and Description. After this follow the individual mice from the two housing conditions: 40 standard housing, 39 enriched housing. Procedure: 80 female isogenic C57BL/6JRj mice (Janvier) were randomly assigned to either standard housing (STD) or environmental enrichment (ENR). The 40 ENR mice were implanted with RFID micro-transponders and housed as one group in a large enriched cage system (ColonyRack, PhenoSys GmbH, Berlin, Germany) composed of 70 interconnected standard cages (7 floors with 10 cages in a double-sided rack). The connector tubes are fitted with ring antennas that collect RFID (radio frequency identification) signals from the mice’s transponder, thus enabling continuous tracking of individual mice. Some of the cages were equipped with tunnels, shelters, and objects that were rearranged regularly to maintain novelty. The 40 STD mice were housed in groups of four per standard cage. Animals entered experimental housing at five weeks of age and remained there for eleven weeks. After housing, hippocampi were dissected, total RNA was isolated, and libraries were sequenced at approximately 40 million reads per sample (DRESDEN-concept Genome Center, Dresden). Raw gene-level counts were imported into R together with sample metadata. Lowly expressed genes were filtered by retaining transcripts with at least 10 reads in at least 39 samples, yielding 17,357 transcripts for downstream analysis. | |
Type of the data | Dataset | |
Total size of the dataset | 18829730 | |
Author | Kempermann, Gerd | |
Author | Rünker, Annette | |
Upload date | 2026-09-28T14:31:51Z | |
Publication date | 2026-09-28T14:31:51Z | |
Data of data creation | 2024 | |
Publication date | 2026-09-28 | |
Abstract of the dataset | Genetically identical mice housed in the same enriched environment (ENR) develop divergent behavioural trajectories associated with differences in adult hippocampal neurogenesis and brain-wide connectivity. We asked whether such inter-individual differences are also reflected in the hippocampal transcriptome—not only as shifts in mean expression, but as effects on within-group variability. Analysing bulk hippocampal RNA-seq from isogenic standard- (STD) and ENR-housed mice, we identified highly variable genes (HVGs) that segregated into common, STD-specific and ENR-specific subsets. ENR did not uniformly increase transcriptional variability: it reduced highest variability in neuron-projection and synapse genes, while maintaining or increasing it in genes linked to extracellular matrix organization and oxidative phosphorylation. Mapped onto a WGCNA-derived ENR co-expression reference, HVGs were unevenly distributed across modules and concentrated at module hubs. Hub architecture and the position of non-hub HVGs differed between modules, corresponding to distinct functional programs: synaptic and chromatin-associated in two, RNA-processing and splicing in a third. Synaptic enrichment in STD-specific HVGs, extracellular-matrix enrichment in common HVGs and module-level localisation were stable across selection thresholds (5–20%). Hippocampal transcriptional variability is thus non-random, functionally coherent, embedded in co-expression architecture and shaped by environmental experience—suggesting it is an undervalued activity-dependent variable in the regulation of brain plasticity. | |
Public reference to this page | https://opara.zih.tu-dresden.de/handle/123456789/2934 | |
Public reference to this page | https://doi.org/10.25532/OPARA-1569 | |
Publisher | Technische Universität Dresden | |
Licence | Attribution-NonCommercial 4.0 International | en |
URI of the licence text | http://creativecommons.org/licenses/by-nc/4.0/ | |
Specification of the discipline(s) | 2::21 | |
Title of the dataset | RNAseq data for Hassani et al. "Environmental enrichment regulates inter-individual transcriptional variance in the hippocampus" | |
Underlying research object | RNAseq data from mice | |
Software | Microsoft Excel | |
Project abstract | Genetically identical mice housed in the same enriched environment (ENR) develop divergent behavioural trajectories associated with differences in adult hippocampal neurogenesis and brain-wide connectivity. We asked whether such inter-individual differences are also reflected in the hippocampal transcriptome—not only as shifts in mean expression, but as effects on within-group variability. Analysing bulk hippocampal RNA-seq from isogenic standard- (STD) and ENR-housed mice, we identified highly variable genes (HVGs) that segregated into common, STD-specific and ENR-specific subsets. ENR did not uniformly increase transcriptional variability: it reduced highest variability in neuron-projection and synapse genes, while maintaining or increasing it in genes linked to extracellular matrix organization and oxidative phosphorylation. Mapped onto a WGCNA-derived ENR co-expression reference, HVGs were unevenly distributed across modules and concentrated at module hubs. Hub architecture and the position of non-hub HVGs differed between modules, corresponding to distinct functional programs: synaptic and chromatin-associated in two, RNA-processing and splicing in a third. Synaptic enrichment in STD-specific HVGs, extracellular-matrix enrichment in common HVGs and module-level localisation were stable across selection thresholds (5–20%). Hippocampal transcriptional variability is thus non-random, functionally coherent, embedded in co-expression architecture and shaped by environmental experience—suggesting it is an undervalued activity-dependent variable in the regulation of brain plasticity. | |
Funding Acknowledgement | This work was supported by VolkswagenFoundation (grant 98 597, “The Mouse in the Supermarket”) and baseline institutional funding. | |
Project title | Environmental enrichment regulates inter-individual transcriptional variance in the hippocampus |
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