type: basic meta: summary: | Zemke et al, Epigenetic and 3D genome reprogramming during the aging of human hippocampus, bioRxiv 2024 description: | The study presents a single-nucleus multiomic analysis of the human hippocampus across adult aging, using tissue from 40 neurotypical donors spanning ages 20 to 100 years. It examines age-associated changes in hippocampal cell populations and their molecular and regulatory states, integrating gene expression, chromatin accessibility, DNA methylation, and 3D genome organization to characterize how the human hippocampus changes across the lifespan. The study uses two complementary assays. 10x Multiome jointly measures gene expression and chromatin accessibility, covering 295,033 nuclei organized into 18 cell subclasses, while snm3C-seq measures DNA methylation and 3D chromatin conformation, covering 22,240 nuclei organized into 13 cell subclasses. Donors were divided into four age groups: 20-40, 40-60, 60-80, and 80-100 years, allowing molecular and regulatory features to be compared across different stages of aging. [Zemke et al, Epigenetic and 3D genome reprogramming during the aging of human hippocampus, bioRxiv 2024.](https://www.biorxiv.org/content/10.1101/2024.10.14.618338v1) 
            zemke2024Epigenetic/
            ├── atac_fragments/                      40 resources
            │   ├── hc11
            │   ├── hc1134
            │   ├── ...
            │   └── hc98
            ├── rna_expression_atac_matrix/          40 resources
            │   ├── hc11
            │   ├── hc1134
            │   ├── ...
            │   └── hc98
            ├── pseudobulk_atac/                     92 resources
            │   ├── Astro/
            │   │   ├── all/
            │   │   ├── age20-40/
            │   │   ├── age40-60/
            │   │   ├── age60-80/
            │   │   └── age80-100/
            │   ├── Astro1/
            │   ├── Astro2/
            │   ├── CA1/
            │   ├── CA2-CA3/
            │   ├── ...
            │   └── VLMC/
            ├── pseudobulk_rna/                      92 resources
            │   ├── Astro/
            │   │   ├── all/
            │   │   ├── age20-40/
            │   │   ├── age40-60/
            │   │   ├── age60-80/
            │   │   └── age80-100/
            │   ├── Astro1/
            │   ├── Astro2/
            │   ├── CA1/
            │   ├── CA2-CA3/
            │   ├── ...
            │   └── VLMC/
            └── supplementary_table/                 24 resources
The data are organized into five main resource groups. **atac\_fragments** and **rna\_expression\_atac\_matrix** each contain 40 donor-level resources, corresponding to the 40 individuals in the study. atac_fragments contains the single-nucleus chromatin-accessibility fragment data generated by 10x Multiome, while rna\_expression\_atac\_matrix contains the corresponding single-nucleus RNA expression matrices. The same donor identifiers are used in both collections. **pseudobulk\_atac** and **pseudobulk\_rna** each contain 92 cell-type- and age-resolved bigWig tracks generated by aggregating nuclei from the corresponding cell populations. The 18 main cell subclasses represented are Astro, CA1, CA2-CA3, Chandelier, DG, Endo, LAMP5, Macro, Microglia, NR2F2, Oligo, OPC, PVALB, SST, SUB, T-Cell, VIP, and VLMC. The GRR also includes four finer, analysis-derived states within the astrocyte and microglia populations: Astro1, Astro2, Micro1, and Micro2. For most of the 18 main subclasses, five pseudobulk tracks are provided: one combining all ages and four corresponding to the age groups age20-40, age40-60, age60-80, and age80-100. CA2-CA3 and DG have only four tracks because the age80-100 group is absent, while the four finer states are represented only by an all track and are not subdivided by age group. This results in 92 pseudobulk ATAC and 92 pseudobulk RNA resources. The **supplementary\_table** collection contains 24 resources corresponding to supplementary tables S1-S24. The snm3C-seq data described in the paper are not included. labels: assay: 10x_Multiome dataset: zemke2024Epigenetic reference_genome: reference/Human/genome/ucsc-hg38 species: human vendor: 10x_Genomics sequencing_platform: Illumina brain_region: hippocampus