IRF3 drives replication stress signaling and determines sensitivity to genotoxic agents in triple-negative breast cancer cells
RNA-seq (gene expression) · human · 12 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
- 12 samples: 3 × HCC38 biol vs 3 × HCC38 IFN-β biol vs 3 × MDA-MB-231 biol vs 3 × MDA-MB-231 IFN-β biolGroups 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.
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 GSE263947_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 PRJNA1100437 and SRA study SRP503273. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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.
- GSM8207836 HCC38 biol rep1 HCC38 biol
- GSM8207837 HCC38 biol rep2 HCC38 biol
- GSM8207838 HCC38 biol rep3 HCC38 biol
- GSM8207839 HCC38 IFN-β biol rep1 HCC38 IFN-β biol
- GSM8207840 HCC38 IFN-β biol rep2 HCC38 IFN-β biol
- GSM8207841 HCC38 IFN-β biol rep3 HCC38 IFN-β biol
- GSM8207842 MDA-MB-231 biol rep1 MDA-MB-231 biol
- GSM8207843 MDA-MB-231 biol rep2 MDA-MB-231 biol
- GSM8207844 MDA-MB-231 biol rep3 MDA-MB-231 biol
- GSM8207845 MDA-MB-231 IFN-β biol rep1 MDA-MB-231 IFN-β biol
- GSM8207846 MDA-MB-231 IFN-β biol rep2 MDA-MB-231 IFN-β biol
- GSM8207847 MDA-MB-231 IFN-β biol rep3 MDA-MB-231 IFN-β biol
- 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
- GSE104675 Role for the Transcriptional Activator ZRF1 in Breast Cancer Progression and Endocrine Resistance 6 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
- GSE11121 The humoral immune system has a key prognostic impact in node-negative breast cancer 200 samples same disease briefing
- GSE322525 PI3K-AKT activation determines oncogenic RAS-induced hypertranscription and replication stress [RNASeq] 18 samples shares replication, determines, stress
- GSE268776 Multi-omics approaches reveal that Diffuse Midline Gliomas are susceptible to replication stress therapy and cholesterol biosynthesis inhibition [RNA-seq] 64 samples shares replication, stress
- GSE320139 The timing of antenatal glucocorticoids determines the receptor sensitivity in preterm infants 47 samples shares sensitivity, determines
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.