Effect of SCN5A depletion on gene expression in xenograft tumours of MDA-MB-231 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: 6 × Control vs 6 × shRNA SCN5AGroups 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
- A novel Na(v)1.5-dependent feedback mechanism driving glycolytic acidification in breast cancer metastasisOncogene · 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 GSE228621_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 PRJNA950459 and SRA study SRP430215. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 2 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.
- GSM7134012 Control 1 Control
- GSM7134013 Control 2 Control
- GSM7134014 Control 3 Control
- GSM7134015 Control 4 Control
- GSM7134016 Control 5 Control
- GSM7134017 Control 6 Control
- GSM7134018 shRNA SCN5A 1 shRNA SCN5A
- GSM7134019 shRNA SCN5A 2 shRNA SCN5A
- GSM7134020 shRNA SCN5A 3 shRNA SCN5A
- GSM7134021 shRNA SCN5A 4 shRNA SCN5A
- GSM7134022 shRNA SCN5A 5 shRNA SCN5A
- GSM7134023 shRNA SCN5A 6 shRNA SCN5A
- 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
- GSE10886 A Supervised Risk Predictor of Breast Cancer Based on Biological Subtypes 226 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
- GSE10885 An integromic analysis reveals that metaplastic carcinomas are distinct from basal-like tumors. 244 samples same disease briefing
- GSE271120 TRAIL-induced cytokine production via NFKB2 pathway promotes neutrophil chemotaxis and immune suppression in triple negative breast cancers [MDA-MB-231] 17 samples shares mda-mb-231, breast
- GSE221833 Next Generation Sequencing Analysis of Breast Cancer Cell Line MCF-7 And MDA-MB-231 After PI3K Inhibition 12 samples shares mda-mb-231, breast
- GSE287572 Transcriptome analysis of triple-negative breast cancer cells HCC1937 and MDA-MB-231 treated with Kalanchoe pinnata (Bryophyllum pinnata) reveals regulation of migration and invasion by downregulation of genes JAK2, ROCK1, ROCK2 and PIK3CA. 12 samples shares mda-mb-231, 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.