Chemotherapy-induced CA-repeat DNA fragments of breast cancer triggers robust immune responses
RNA-seq (gene expression) · human · 20 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)
- Topic
- Breast cancerThis series is part of our curated briefing on it.
- Samples
- 20 samples: 10 × IM-group vs 5 × IS-group vs 5 × IP-groupGroups 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.
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 GSE302920_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 PRJNA1292839 and SRA study SRP601575. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 20 samples.
How we read this: 3 replicated groups read from 20 sample titles; they account for 20 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.
- GSM9113670 IS-group1 IS-group
- GSM9113671 IS-group2 IS-group
- GSM9113672 IS-group3 IS-group
- GSM9113673 IS-group4 IS-group
- GSM9113674 IS-group5 IS-group
- GSM9113675 IM-group1 IM-group
- GSM9113676 IM-group2 IM-group
- GSM9113677 IM-group3 IM-group
- GSM9113678 IM-group4 IM-group
- GSM9113679 IM-group5 IM-group
- GSM9113680 IM-group6 IM-group
- GSM9113681 IM-group7 IM-group
- GSM9113682 IM-group8 IM-group
- GSM9113683 IM-group9 IM-group
- GSM9113684 IM-group10 IM-group
- GSM9113685 IP-group1 IP-group
- GSM9113686 IP-group2 IP-group
- GSM9113687 IP-group3 IP-group
- GSM9113688 IP-group4 IP-group
- GSM9113689 IP-group5 IP-group
- 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
- GSE11121 The humoral immune system has a key prognostic impact in node-negative breast cancer 200 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
- GSE10885 An integromic analysis reveals that metaplastic carcinomas are distinct from basal-like tumors. 244 samples same disease briefing
- GSE236783 RNA-seq gene expression profile of SUM159PT breast cancer cell line upon manipulation of two TDMD triggers, NREP and SERPINE1 16 samples shares triggers, breast
- GSE280204 Ferroptotic neutrophils eradicate chemotherapy-induced immunity in breast cancer (Neutrophils) 10 samples shares chemotherapy-induced, breast
- GSE303589 Ellagic Acid as a Novel YTHDF Inhibitor Triggers Tumor-Suppressive in Triple-Negative Breast Cancer I 9 samples shares triggers, 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.