Spatial transcriptomics of triple negative breast cancer
Spatial transcriptomics · human · 43 samples
- What it is
- Spatial transcriptomicsGene activity measured with its position in a tissue section.
- Organism
- Homo sapiens (human)
- Topic
- Breast cancerThis series is part of our curated briefing on it.
- Samples
- 43 samples: 21 conditions, mostly in duplicateGroups 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.
Direct links to NCBI, 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.
Whole study · RAW.tar
Everything the authors deposited as one archive (GSE210616_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.
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 PRJNA866496. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 42 samples.
How we read this: 21 replicated groups read from 43 sample titles; they account for 42 of them. 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.
- GSM6433585 Primary TNBC, patient 9, section 1 Primary TNBC, patient 9…
- GSM6433586 Primary TNBC, patient 9, section 2 Primary TNBC, patient 9…
- GSM6433587 Primary TNBC, patient 11, section 1 Primary TNBC, patient 1…
- GSM6433588 Primary TNBC, patient 11, section 2 Primary TNBC, patient 1…
- GSM6433589 Primary TNBC, patient 12, section 1 Primary TNBC, patient 1…
- GSM6433590 Primary TNBC, patient 12, section 2 Primary TNBC, patient 1…
- GSM6433591 Primary TNBC, patient 13, section 1 Primary TNBC, patient 1…
- GSM6433592 Primary TNBC, patient 13, section 2 Primary TNBC, patient 1…
- GSM6433593 Primary TNBC, patient 14, section 1 Primary TNBC, patient 1…
- GSM6433594 Primary TNBC, patient 14, section 2 Primary TNBC, patient 1…
- GSM6433595 Primary TNBC, patient 15, section 1 Primary TNBC, patient 1…
- GSM6433596 Primary TNBC, patient 15, section 2 Primary TNBC, patient 1…
- GSM6433597 Primary TNBC, patient 1, section 1 Primary TNBC, patient 1…
- GSM6433598 Primary TNBC, patient 1, section 2 Primary TNBC, patient 1…
- GSM6433599 Primary TNBC, patient 2, section 1 Primary TNBC, patient 2…
- GSM6433600 Primary TNBC, patient 2, section 2 Primary TNBC, patient 2…
- GSM6433601 Primary TNBC, patient 3, section 1 Primary TNBC, patient 3…
- GSM6433602 Primary TNBC, patient 3, section 2 Primary TNBC, patient 3…
- GSM6433603 Primary TNBC, patient 4, section 1 Primary TNBC, patient 4…
- GSM6433604 Primary TNBC, patient 4, section 2 Primary TNBC, patient 4…
- GSM6433605 Primary TNBC, patient 5, section 1 Primary TNBC, patient 5…
- GSM6433606 Primary TNBC, patient 5, section 2 Primary TNBC, patient 5…
- GSM6433607 Primary TNBC, patient 6, section 1 Primary TNBC, patient 6…
- GSM6433608 Primary TNBC, patient 6, section 2 Primary TNBC, patient 6…
- GSM6433609 Primary TNBC, patient 7, section 1 Primary TNBC, patient 7…
- GSM6433610 Primary TNBC, patient 7, section 2 Primary TNBC, patient 7…
- GSM6433611 Primary TNBC, patient 8, section 1 Primary TNBC, patient 8…
- GSM6433612 Primary TNBC, patient 8, section 2 Primary TNBC, patient 8…
- GSM6433613 Primary TNBC, patient 17, section 1 Primary TNBC, patient 1…
- GSM6433614 Primary TNBC, patient 17, section 2 Primary TNBC, patient 1…
- GSM6433615 Primary TNBC, patient 18, section 1 Primary TNBC, patient 1…
- GSM6433616 Primary TNBC, patient 18, section 2 Primary TNBC, patient 1…
- GSM6433617 Primary TNBC, patient 19, section 1
- GSM6433618 Primary TNBC, patient 20, section 1 Primary TNBC, patient 2…
- GSM6433619 Primary TNBC, patient 20, section 2 Primary TNBC, patient 2…
- GSM6433620 Primary TNBC, patient 21, section 1 Primary TNBC, patient 2…
- GSM6433621 Primary TNBC, patient 21, section 2 Primary TNBC, patient 2…
- GSM6433622 Primary TNBC, patient 22, section 1 Primary TNBC, patient 2…
- GSM6433623 Primary TNBC, patient 22, section 2 Primary TNBC, patient 2…
- GSM6433624 Primary TNBC, patient 23, section 1 Primary TNBC, patient 2…
+ 3 more — browse all 43 samples with per-sample file links →
- GSE11121 The humoral immune system has a key prognostic impact in node-negative breast cancer 200 samples same disease briefing · shares negative, breast
- GSE10886 A Supervised Risk Predictor of Breast Cancer Based on Biological Subtypes 226 samples same disease briefing · shares breast
- 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
- GSE10885 An integromic analysis reveals that metaplastic carcinomas are distinct from basal-like tumors. 244 samples same disease briefing
- GSE169246 PD-L1 blockade-induced temporal single cell dynamics in triple negative breast cancer 83 samples shares negative, triple, breast
- 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 negative, triple, breast
- GSE303346 Single-Cell RNA-Seq Reveals Immunosuppressive Effects of Triple-Negative Breast Cancer–Derived Exosomes on NK Cell Responses 16 samples shares negative, triple, breast
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.