RNAseq analysis of chemotherapy and radiation therapy-naïve breast tumors
RNA-seq (gene expression) · human · 103 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Homo sapiens (human)
- Samples
- 103 samples
- 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.
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 GSE100925_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA393443 and SRA study SRP111343. Searching any of these in the dataset finder brings you back here.
The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.
+ 103 more — browse all 103 samples with per-sample file links →
- GSE309004 Molecular determinants of neoadjuvant chemotherapy resistance in breast cancer: An analysis of gene expression and tumor microenvironment 54 samples shares chemotherapy, breast
- GSE205472 A Single-Cell Atlas of HR+ Breast Cancer Reveals the Shifting of the Tumor Microenvironment in Response to Neoadjuvant Chemotherapy 13 samples shares chemotherapy, breast
- GSE25066 Genomic predictor of response and survival following neoadjuvant taxane-anthracycline chemotherapy in breast cancer 508 samples shares chemotherapy, breast
- GSE25065 Validation cohort for genomic predictor of response and survival following neoadjuvant taxane-anthracycline chemotherapy in breast cancer 198 samples shares chemotherapy, breast
- GSE325047 Pervasive Enhanced Transcription in Inflammatory Breast Cancer Tumors and PBMCs Impacts RNA Splicing and Intronic RNAs in Plasma 80 samples shares breast
- GSE222556 Neoadjuvant PARPi or Chemotherapy in Ovarian Cancer Informs Targeting Effector Treg Cells for Homologous-Recombination-Deficient Tumors [10x scRNA-seq] 67 samples shares chemotherapy
- GSE269793 Neoadjuvant PARPi or Chemotherapy in Ovarian Cancer Informs Targeting Effector Treg Cells for Homologous-Recombination-Deficient Tumors [Singleron scRNA-seq] 10 samples shares chemotherapy
- GSE283522 The spatially informed mFISHseq assay resolves biomarker discordance and predicts treatment response in breast cancer 1254 samples shares 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.