RNA-seq analysis for MDA-MB-468 cells treated with SAHA and sonidedgib
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 × Con vs 3 × SAHA vs 3 × sonidedgib vs 3 × SAHA+sonidedgibGroups 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 GSE187427_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 PRJNA777563 and SRA study SRP344377. 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.
- GSM5668311 Con_1 Con
- GSM5668312 Con_2 Con
- GSM5668313 Con_3 Con
- GSM5668314 SAHA_1 SAHA
- GSM5668315 SAHA_2 SAHA
- GSM5668316 SAHA_3 SAHA
- GSM5668317 sonidedgib_1 sonidedgib
- GSM5668318 sonidedgib_2 sonidedgib
- GSM5668319 sonidedgib_3 sonidedgib
- GSM5668320 SAHA+sonidedgib_1 SAHA+sonidedgib
- GSM5668321 SAHA+sonidedgib_2 SAHA+sonidedgib
- GSM5668322 SAHA+sonidedgib_3 SAHA+sonidedgib
- 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
- GSE296117 A single-cell RNA-seq dataset of synovial fluid from rheumatoid arthritis treated with TNF-α/JAK inhibitor 18 samples shares rna-seq, treated
- GSE272346 Late-stage tertiary lymphoid structures in hepatocellular carcinoma treated with neoadjuvant immune checkpoint blockade [bulk RNA-seq] 14 samples shares rna-seq, treated
- GSE309595 Longitudinal Analysis of Multiple Myeloma: Therapeutic Response and Immune Microenvironment Dynamics in the Context of Tumor Heterogeneity [scRNA-seq] 270 samples shares rna-seq
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.