TWEAK/Fn14 signalling in Breast Cancer (RNA-Seq)
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)
- Samples
- 12 samples: 3 × SKBR3_UT vs 3 × SKBR3_TWEAK vs 3 × MB453_UT vs 3 × MB453_TWEAKGroups 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
- TWEAK/Fn14 signalling driven super-enhancer reprogramming promotes pro-metastatic metabolic rewiring in triple-negative breast cancerNature communications · 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 GSE251869_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 PRJNA1055578 and SRA study SRP479509. 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.
- GSM7989329 SKBR3_UT_rep1 SKBR3_UT
- GSM7989330 SKBR3_UT_rep2 SKBR3_UT
- GSM7989331 SKBR3_UT_rep3 SKBR3_UT
- GSM7989332 SKBR3_TWEAK_rep1 SKBR3_TWEAK
- GSM7989333 SKBR3_TWEAK_rep2 SKBR3_TWEAK
- GSM7989334 SKBR3_TWEAK_rep3 SKBR3_TWEAK
- GSM7989335 MB453_UT_rep1 MB453_UT
- GSM7989336 MB453_UT_rep2 MB453_UT
- GSM7989337 MB453_UT_rep3 MB453_UT
- GSM7989338 MB453_TWEAK_rep1 MB453_TWEAK
- GSM7989339 MB453_TWEAK_rep2 MB453_TWEAK
- GSM7989340 MB453_TWEAK_rep3 MB453_TWEAK
- GSE319641 RNA-Seq profiling of pre- and on-treatment tumor samples from breast cancer patients enrolled in the NeoTRIP trial. 401 samples shares rna-seq, breast
- GSE261713 Linking single cell genomes and transcriptomes at scale to decode breast cancer progression [scRNA-seq] 35 samples shares rna-seq, breast
- GSE303346 Single-Cell RNA-Seq Reveals Immunosuppressive Effects of Triple-Negative Breast Cancer–Derived Exosomes on NK Cell Responses 16 samples shares rna-seq, breast
- GSE245414 RNA-seq profiling of breast metastases from different sites 42 samples shares rna-seq, breast
- GSE323973 Expression profiling by high throughput sequencing of breast cancer 158 samples shares breast
- GSE270680 A spatially resolved atlas of gastric cancer characterises a lymphocyte aggregated region [scRNA-seq] 77 samples shares rna-seq
- GSE292858 RNA-Seq analysis of tumor and matched normal samples from colorectal cancer patients. 73 samples shares rna-seq
- GSE222556 Neoadjuvant PARPi or Chemotherapy in Ovarian Cancer Informs Targeting Effector Treg Cells for Homologous-Recombination-Deficient Tumors [10x scRNA-seq] 67 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.