TWEAK/Fn14 signalling in Breast Cancer [cell line RNA-seq]
RNA-seq (gene expression) · human · 24 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
- 24 samples: 8 conditions, mostly in triplicateGroups 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 GSE231480_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 PRJNA966127 and SRA study SRP435576. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 24 samples.
How we read this: 8 replicated groups read from 24 sample titles; they account for 24 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.
- GSM7286612 MB231_UT_RNA-seq_rep1 MB231_UT_RNA-seq
- GSM7286613 MB231_UT_RNA-seq_rep2 MB231_UT_RNA-seq
- GSM7286614 MB231_UT_RNA-seq_rep3 MB231_UT_RNA-seq
- GSM7286615 MB231_TWEAK_RNA-seq_rep1 MB231_TWEAK_RNA-seq
- GSM7286616 MB231_TWEAK_RNA-seq_rep2 MB231_TWEAK_RNA-seq
- GSM7286617 MB231_TWEAK_RNA-seq_rep3 MB231_TWEAK_RNA-seq
- GSM7286618 Hs578T_UT_RNA-seq_rep1 Hs578T_UT_RNA-seq
- GSM7286619 Hs578T_UT_RNA-seq_rep2 Hs578T_UT_RNA-seq
- GSM7286620 Hs578T_UT_RNA-seq_rep3 Hs578T_UT_RNA-seq
- GSM7286621 Hs578T_TWEAK_RNA-seq_rep1 Hs578T_TWEAK_RNA-seq
- GSM7286622 Hs578T_TWEAK_RNA-seq_rep2 Hs578T_TWEAK_RNA-seq
- GSM7286623 Hs578T_TWEAK_RNA-seq_rep3 Hs578T_TWEAK_RNA-seq
- GSM7286624 MCF7_UT_RNA-seq_rep1 MCF7_UT_RNA-seq
- GSM7286625 MCF7_UT_RNA-seq_rep2 MCF7_UT_RNA-seq
- GSM7286626 MCF7_UT_RNA-seq_rep3 MCF7_UT_RNA-seq
- GSM7286627 MCF7_TWEAK_RNA-seq_rep1 MCF7_TWEAK_RNA-seq
- GSM7286628 MCF7_TWEAK_RNA-seq_rep2 MCF7_TWEAK_RNA-seq
- GSM7286629 MCF7_TWEAK_RNA-seq_rep3 MCF7_TWEAK_RNA-seq
- GSM7286630 CAMA1_UT_RNA-seq_rep1 CAMA1_UT_RNA-seq
- GSM7286631 CAMA1_UT_RNA-seq_rep2 CAMA1_UT_RNA-seq
- GSM7286632 CAMA1_UT_RNA-seq_rep3 CAMA1_UT_RNA-seq
- GSM7286633 CAMA1_TWEAK_RNA-seq_rep1 CAMA1_TWEAK_RNA-seq
- GSM7286634 CAMA1_TWEAK_RNA-seq_rep2 CAMA1_TWEAK_RNA-seq
- GSM7286635 CAMA1_TWEAK_RNA-seq_rep3 CAMA1_TWEAK_RNA-seq
- 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
- GSE25066 Genomic predictor of response and survival following neoadjuvant taxane-anthracycline chemotherapy in breast cancer 508 samples shares breast, line
- GSE245414 RNA-seq profiling of breast metastases from different sites 42 samples shares rna-seq, 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 rna-seq
- GSE269877 Single-cell RNA-sequencing of BCG naïve and recurrent non-muscle invasive bladder cancer reveals a CD6/ALCAM-mediated immune-suppressive pathway 38 samples shares rna-seq
- GSE294300 Single-cell gene expression profiles of cells from primary colorectal cancer and adjacent normal tissue [scRNA-Seq] 36 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.