Single cell lineage tracing reveals clonal dynamics of anti-EGFR therapy resistance in triple negative breast cancer.
Single-cell RNA-seq · human · 16 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
- Organism
- Homo sapiens (human)
- Topic
- Breast cancerThis series is part of our curated briefing on it.
- Samples
- 16 samples: 12 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
- Single cell lineage tracing reveals clonal dynamics of anti-EGFR therapy resistance in triple negative breast cancerGenome medicine · 2024
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 GSE228382_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 PRJNA949598 and SRA study SRP429142. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 16 sample titles: 12 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.
- GSM7115639 468, Day0, replicate1, scRNAseq
- GSM7115640 468, Day0, replicate2, scRNAseq
- GSM7115641 468, Day3, Afatinib, scRNAseq
- GSM7115642 468, Day6, Afatinib, scRNAseq
- GSM7115643 468, Day9, Afatinib, scRNAseq
- GSM7118094 MDAMB468, Control, replicate 1
- GSM7118095 MDAMB468, Control, replicate 2
- GSM7118096 MDAMB468, Control, replicate 3
- GSM7118097 MDAMB468, IGFBP2 over-expression, replicate 1
- GSM7118098 MDAMB468, IGFBP2 over-expression, replicate 2
- GSM7118099 MDAMB468, IGFBP2 over-expression, replicate 3
- GSM7118110 SUM149PT
- GSM7118111 SUM159PT
- GSM7118112 SUM185PE
- GSM7118113 SUM229PE
- GSM7118114 SUM1315MO2
- GSE104675 Role for the Transcriptional Activator ZRF1 in Breast Cancer Progression and Endocrine Resistance 6 samples same disease briefing · shares resistance
- GSE11121 The humoral immune system has a key prognostic impact in node-negative breast cancer 200 samples same disease briefing · shares negative
- 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
- GSE10885 An integromic analysis reveals that metaplastic carcinomas are distinct from basal-like tumors. 244 samples same disease briefing
- GSE10886 A Supervised Risk Predictor of Breast Cancer Based on Biological Subtypes 226 samples same disease briefing
- GSE315928 Differential T cell clonal dynamics underlie outcomes to frontline chemoimmunotherapy in advanced gastric cancer [paired scRNA/TCR-seq] 94 samples shares dynamics, therapy, clonal
- GSE300628 HER2 heterogeneous breast cancer models reveal novel therapeutic targets and subclonal dynamics during evolution to resistance to HER2-targeted therapies 60 samples shares resistance, dynamics, clonal
- GSE291679 Lineage Tracing Reveals Clone-Specific Responses to Doxorubicin in Triple-Negative Breast Cancer 36 samples shares negative, lineage, tracing
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.