scRNA-seq, snATAC-seq, and spatial transcriptomics analysis of mammary glands of aged female mice
Spatial transcriptomics · mouse · 22 samples
- What it is
- Spatial transcriptomicsGene activity measured with its position in a tissue section.
- Organism
- Mus musculus (mouse)
- Samples
- 22 samples: 20 distinct titles, 2 of them repeatedGroups are read from the sample names, not from the paper. Check the list below.
- Data you can get
- A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
- Paper
- Comprehensive single-cell aging atlas of healthy mammary tissues reveals shared epigenomic and transcriptomic signatures of aging and cancerNature aging · 2025
Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.
Processed table
The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE216542_RAW.tar (it can run to tens of gigabytes).
Raw sequencing reads
The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.
What the files usually look like: Spatial studies usually ship Space Ranger style folders (count matrix plus tissue images). Look for them among the supplementary files.
Also filed as BioProject PRJNA894189 and SRA study SRP404481. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 22 sample titles: 20 distinct titles with little repetition. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.
- GSM6678930 OA20001, Mammary Glands Cells, rep4, 3months, scRNAseq
- GSM6678931 OA20002, Mammary Glands Cells, rep4, 18months, scRNAseq
- GSM6678932 OA20003, Mammary Glands Cells, rep5, 3months, scRNAseq
- GSM6678933 OA20004, Mammary Glands Cells, rep5, 18months, scRNAseq
- GSM6678934 OA20005, Mammary Glands Cells, rep6, 3months, scRNAseq
- GSM6678935 OA20006, Mammary Glands Cells, rep6, 18months, scRNAseq
- GSM6678936 OA20011, Mammary Glands Cells, rep1, 3months, scRNAseq
- GSM6678937 OA20013, Mammary Glands Cells, rep1, 18months, scRNAseq
- GSM6678938 OA20015, Mammary Glands Cells, rep2, 3months, scRNAseq
- GSM6678939 OA20017, Mammary Glands Cells, rep2, 18months, scRNAseq
- GSM6678940 OA20019, Mammary Glands Cells, rep3, 3months, scRNAseq
- GSM6678941 OA20021, Mammary Glands Cells, rep3, 18months, scRNAseq
- GSM6678942 OA20012, Mammary Glands Cells, rep1, 3months, snATACseq
- GSM6678943 OA20014, Mammary Glands Cells, rep1, 18months, snATACseq
- GSM6678944 OA20016, Mammary Glands Cells, rep2, 3months, snATACseq
- GSM6678945 OA20018, Mammary Glands Cells, rep2, 18months, snATACseq
- GSM6678946 OA20020, Mammary Glands Cells, rep3, 3months, snATACseq
- GSM6678947 OA20022, Mammary Glands Cells, rep3, 18months, snATACseq
- GSM7837730 Mammary Glands Cells, 18M, ST, Rep1
- GSM7837731 Mammary Glands Cells, 18M, ST, Rep2
- GSM8155366 Mammary Glands Cells, 3M, Rep1
- GSM8155367 Mammary Glands Cells, 3M, Rep2
- GSE300288 Single-cell and spatial transcriptomics analysis of tobacco-associated lung adenocarcinoma development, and in response to targeting inflammation alone or in combination with immune checkpoint blockade in precancerous phase [scRNA-seq] 31 samples shares scrna-seq, spatial
- GSE297388 Spatial transcriptomics and scRNA-sequencing on gastrocnemius muscle form B6-mdx and D2-mdx mice 8 samples shares scrna-seq, spatial
- GSE277228 Changing dynamics of the fibroblast differentiation hierarchy during mammary gland morphogenesis and tumorigenesis [scRNA-Seq I] 13 samples shares scrna-seq, mammary
- GSE268876 Spatially clustered type I interferon responses at injury borderzones [scRNA-Seq] 12 samples shares scrna-seq, spatial
- GSE264105 Plate-based scRNA-seq of plasma-positive microglia and plasma-negative microglia in young mice 1111 samples shares scrna-seq
- GSE271100 Stem cells tightly regulate dead cell clearance to maintain tissue fitness [scRNA-seq] 1037 samples shares scrna-seq
- GSE326100 scRNA-seq of mouse cochlea organoid cells 768 samples shares scrna-seq
- GSE255371 Characterization of cuprizone mouse model at single-cell and spatial transcriptomics level 86 samples shares spatial
Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.