GEO series
Single nuclei chromatin accessibility and transcriptomic map of breast tissues of women of diverse genetic ancestry [10X single-cell multiome]
GSE244585
Homo sapiens
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
32 samples
Submitted 2024/04/19
Platform GPL24676
Summary
Single nuclei analysis is allowing robust classification of cell types in an organ that helps to establish relationships between cell-type specific gene expression and chromatin accessibility status of gene regulatory regions. Using breast tissues of 92 healthy donors of various genetic ancestry, we have developed a comprehensive chromatin accessibility and gene expression atlas of human breast tissues. Integrated analysis revealed 10 distinct cell types in the healthy breast, which included three major epithelial cell subtypes (luminal-hormone sensing, luminal adaptive secretory precursor, and basal-myoepithelial cells), two endothelial subtypes, two adipocyte subtypes, fibroblasts, T-cells, and macrophages. By integrating gene expression signatures derived from epithelial cell subtypes with spatial transcriptomics, we identify specific gene expression differences between lobular and ductal epithelial cells and age-associated changes in epithelial cell gene expression patterns and signaling networks. Among various cell types, luminal adaptive secretory cells and fibroblasts showed genetic ancestry dependent variability as a subpopulation of luminal adaptive secretory cells with alveolar progenitor (AP) cell state were enriched in Indigenous American (IA) ancestry and fibroblast populations were distinct in African ancestry. ESR1 expression pattern was distinctly different in tissues from IA compared to the rest, with a high level of ESR1 expression extending to AP cells and crosstalk between growth factors and Estrogen Receptor signaling is evident in these AP cells. In general, cell subtype-specific gene expression did not correlate with chromatin accessibility differences, suggesting that transcriptional regulation independent of chromatin accessibility governs cell type-specific gene expression in the breast.
This dataset
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Direct links to NCBI, no account and no request form: the whole study as GSE244585_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 32 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA1023624 and SRA study SRP464412. Searching any of these in the dataset finder brings you back here.
Study design
32 conditions, each sampled once — no replicated groups
Read from 32 sample titles: 32 distinct titles with little repetition. Check it against the sample list below before relying on it.
Samples in this study
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- GSM7821192 Ashkenazi_NormalBreastSample_multiome_Pool1, scATAC-seq
- GSM7821193 KTB_pool-3-Ashkenazi_jew, scATAC-seq
- GSM7821194 KTB_pool-4-Ashkenazi_jew, scATAC-seq
- GSM7821195 KTBpool5_Ashkenazi_jew, scATAC-seq
- GSM7821196 KTBpool6_Ashkenazi_jew, scATAC-seq
- GSM7821197 Pool7_BRCA2Positive, scATAC-seq
- GSM7821198 Pool8_BRCA1Positive, scATAC-seq
- GSM7821199 KTBpool9-White American, scATAC-seq
- GSM7821200 KTBpool11-White American, scATAC-seq
- GSM7821201 KTBpool12-White American, scATAC-seq
- GSM7821202 KTBpool_13-Indigenous American, scATAC-seq
- GSM7821203 KTBpool_14-Indigenous American, scATAC-seq
- GSM7821204 KTBpool15_Asian, scATAC-seq
- GSM7821205 KTBpool17_Asian, scATAC-seq
- GSM7821206 C23_KTBpool-23_Hispanic, scATAC-seq
- GSM7821207 C25_KTBpool-25_Hispanic, scATAC-seq
- GSM7821208 Ashkenazi_NormalBreastSample_multiome_Pool1, scRNA-seq
- GSM7821209 KTB_pool-3-Ashkenazi_jew, scRNA-seq
- GSM7821210 KTB_pool-4-Ashkenazi_jew, scRNA-seq
- GSM7821211 KTBpool5_Ashkenazi_jew, scRNA-seq
- GSM7821212 KTBpool6_Ashkenazi_jew, scRNA-seq
- GSM7821213 Pool7_BRCA2Positive, scRNA-seq
- GSM7821214 Pool8_BRCA1Positive, scRNA-seq
- GSM7821215 KTBpool9-White American, scRNA-seq
- GSM7821216 KTBpool11-White American, scRNA-seq
- GSM7821217 KTBpool12-White American, scRNA-seq
- GSM7821218 KTBpool_13-Indigenous American, scRNA-seq
- GSM7821219 KTBpool_14-Indigenous American, scRNA-seq
- GSM7821220 KTBpool15_Asian, scRNA-seq
- GSM7821221 KTBpool17_Asian, scRNA-seq
- GSM7821222 C23_KTBpool-23_Hispanic, scRNA-seq
- GSM7821223 C25_KTBpool-25_Hispanic, scRNA-seq
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