Breast cancer remodels lymphatics in sentinel lymph nodes
Single-cell RNA-seq · human · 22 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
- Organism
- Homo sapiens (human)
- Topic
- Breast cancerThis series is part of our curated briefing on it.
- Samples
- 22 samples: 22 samples, each with a distinct title — no replicated groupsGroups 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
- Breast cancer remodels lymphatics in sentinel lymph nodesNature communications · 2025
Read the full summary ↓
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 GSE248214_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.
Also filed as BioProject PRJNA1042832 and SRA study SRP472890. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 22 sample titles: 22 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.
- GSM7908437 patient 1, AXLN1 LEC, metastatic
- GSM7908438 patient 1, AXLN2 LEC, metastatic
- GSM7908439 patient 1, AXLN3 LEC, metastatic
- GSM7908440 patient 1, AXLN4 LEC, metastatic
- GSM7908441 patient 2, AXLN1 LEC, metastatic
- GSM7908442 patient 3, AXLN1 LEC, metastatic
- GSM7908443 patient 3, AXLN2 LEC, non-metastatic
- GSM7908444 patient 4, AXLN1 LEC, metastatic
- GSM7908445 patient 4, AXLN2 LEC, non-metastatic
- GSM7908446 patient 5, AXLN1 LEC, metastatic
- GSM7908447 patient 5, AXLN2 LEC, non-metastatic
- GSM7908448 patient 5, AXLN3 LEC, non-metastatic
- GSM7908449 patient 5, AXLN4 LEC, metastatic
- GSM7908450 patient 6, AXLN1 LEC, metastatic
- GSM7908451 patient 6, AXLN2 LEC, metastatic
- GSM7908452 patient 6, AXLN3 LEC, non-metastatic
- GSM7908453 patient 7, AXLN1 LEC, metastatic
- GSM7908454 patient 7, AXLN2 LEC, non-metastatic
- GSM7908455 patient 8, AXLN1 LEC, metastatic
- GSM7908456 patient 8, AXLN2 LEC, non-metastatic
- GSM7908457 patient 9, AXLN1 LEC, metastatic
- GSM7908458 patient 9, AXLN2 LEC, non-metastatic
- GSE104193 Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-β signalling and malignant features in vitro and in vivo 32 samples same disease briefing · shares breast
- GSE104675 Role for the Transcriptional Activator ZRF1 in Breast Cancer Progression and Endocrine Resistance 6 samples same disease briefing · shares breast
- GSE10886 A Supervised Risk Predictor of Breast Cancer Based on Biological Subtypes 226 samples same disease briefing · shares breast
- GSE11121 The humoral immune system has a key prognostic impact in node-negative breast cancer 200 samples same disease briefing · shares breast
- GSE10885 An integromic analysis reveals that metaplastic carcinomas are distinct from basal-like tumors. 244 samples same disease briefing
- GSE328275 Single-cell RNA sequencing of CD45+ immune cells across primary tumor, sentinel tumor-draining lymph node, and axillary lymph node in treatment-naive triple-negative breast cancer 28 samples shares sentinel, breast, lymph
- GSE253036 Tumor Cell JAGGED-1 Promotes Lymph Node Metastasis and Predicts Recurrence in Lymph Node Positive Breast Cancer Patients 27 samples shares breast, lymph
- GSE261774 SPP1+ macrophages in HR+ breast cancer are associated with tumour-infiltrating lymphocytes. 21 samples shares breast, lymph
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.