Gene Expression Changes Induced by YTHDC1 knockdown 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 × MDA-MB-231, siNC, vs 3 × MDA-MB-231, siYTHDC1, vs 3 × Hs578T, siNC, vs 3 × Hs578T, siYTHDC1,Groups 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.
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 GSE317469_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 PRJNA1413175 and SRA study SRP665932. 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.
- GSM9472767 MDA-MB-231, siNC, rep1 MDA-MB-231, siNC,
- GSM9472768 MDA-MB-231, siNC, rep2 MDA-MB-231, siNC,
- GSM9472769 MDA-MB-231, siNC, rep3 MDA-MB-231, siNC,
- GSM9472770 MDA-MB-231, siYTHDC1, rep1 MDA-MB-231, siYTHDC1,
- GSM9472771 MDA-MB-231, siYTHDC1, rep2 MDA-MB-231, siYTHDC1,
- GSM9472772 MDA-MB-231, siYTHDC1, rep3 MDA-MB-231, siYTHDC1,
- GSM9472773 Hs578T, siNC, rep1 Hs578T, siNC,
- GSM9472774 Hs578T, siNC, rep2 Hs578T, siNC,
- GSM9472775 Hs578T, siNC, rep3 Hs578T, siNC,
- GSM9472776 Hs578T, siYTHDC1, rep1 Hs578T, siYTHDC1,
- GSM9472777 Hs578T, siYTHDC1, rep2 Hs578T, siYTHDC1,
- GSM9472778 Hs578T, siYTHDC1, rep3 Hs578T, siYTHDC1,
- 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
- GSE304137 Macrophage and Triple-Negative Breast Cancer Cell Phenotype Changes in a 3D Co-Culture Model 24 samples shares triple-negative, changes, breast
- GSE263995 Gene expression at single cell level of tumor-infiltrating cells from the tumor foci, draining lymph node and peripheral blood of triple-negative breast cancer 14 samples shares triple-negative, breast
- GSE334033 A Patient-Derived Xenograft Model Identifies AK1 as a Key Regulator of Metastatic Potential in Primary Triple-Negative Breast Cancer 105 samples shares triple-negative, 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.