SPP1+ macrophages in HR+ breast cancer are associated with tumour-infiltrating lymphocytes.
Single-cell RNA-seq · human · 21 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
- 21 samples: 21 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
- SPP1+ macrophages in HR+ breast cancer are associated with tumor-infiltrating lymphocytesNPJ breast cancer · 2024
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 GSE261774_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 PRJNA1088841 and SRA study SRP495941. 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 21 sample titles: 21 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.
- GSM8151500 BC17079, scRNAseq
- GSM8151501 BC17080, scRNAseq
- GSM8151502 BC17083, scRNAseq
- GSM8151503 BC17087, scRNAseq
- GSM8151504 BC17100, scRNAseq
- GSM8151505 BC17114, scRNAseq
- GSM8151506 BC17121, scRNAseq
- GSM8151507 BC17122, scRNAseq
- GSM8151508 BC17134, scRNAseq
- GSM8151509 BC17140, scRNAseq
- GSM8151510 BC17146, scRNAseq
- GSM8151511 BC17148, scRNAseq
- GSM8151512 BC17157, scRNAseq
- GSM8151513 BC17166, scRNAseq
- GSM8151514 BC17172, scRNAseq
- GSM8151515 BC18050, scRNAseq
- GSM8151516 BC18051, scRNAseq
- GSM8151517 BC19104, scRNAseq
- GSM8151518 BC19108, scRNAseq
- GSM8151519 BC19115, scRNAseq
- GSM8151520 BC19127, scRNAseq
- 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
- GSE252465 Early-stage idiopathic pulmonary fibrosis is characterized by bronchoalveolar accumulation of SPP1+ macrophages 16 samples shares spp1, macrophages
- GSE342455 Transcriptomic profiling of tumor-associated macrophages following pharmacological SYK inhibition in a human breast cancer co-culture model 6 samples shares macrophages, breast
- GSE335667 Predicting relevant microglia-associated cell-cell communication pathways in Alzheimer’s disease: a role for SPP1 10 samples shares spp1
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.