HOTAIR-YTHDF3 interaction in promoting breast cancer cell metastasis [RNA-seq]
RNA-seq (gene expression) · human · 22 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
- 22 samples: 11 conditions, mostly in duplicateGroups 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 GSE215289_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 PRJNA889709 and SRA study SRP402110. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 22 samples.
How we read this: 11 replicated groups read from 22 sample titles; they account for 22 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.
- GSM6631263 RNA C-NT-1-1-Rep1 RNA C-NT-1-1
- GSM6631264 RNA C-NT-1-1-Rep2 RNA C-NT-1-1
- GSM6631265 RNA C-P18-Rep1 RNA C-P18
- GSM6631266 RNA C-P18-Rep2 RNA C-P18
- GSM6631267 RNA C-puro-8-Rep1 RNA C-puro-8
- GSM6631268 RNA C-puro-8-Rep2 RNA C-puro-8
- GSM6631269 RNA C-YTHDF3-2-Rep1 RNA C-YTHDF3-2
- GSM6631270 RNA C-YTHDF3-2-Rep2 RNA C-YTHDF3-2
- GSM6631271 RNA C-YTHDF3-4-Rep1 RNA C-YTHDF3-4
- GSM6631272 RNA C-YTHDF3-4-Rep2 RNA C-YTHDF3-4
- GSM6631273 RNA OE-P18-Rep1 RNA OE-P18
- GSM6631274 RNA OE-P18-Rep2 RNA OE-P18
- GSM6631275 RNA OE-puro-3-Rep1 RNA OE-puro-3
- GSM6631276 RNA OE-puro-3-Rep2 RNA OE-puro-3
- GSM6631277 RNA OE-YTHDF3-5-Rep1 RNA OE-YTHDF3-5
- GSM6631278 RNA OE-YTHDF3-5-Rep2 RNA OE-YTHDF3-5
- GSM6631279 RNA OE-YTHDF3-1-Rep1 RNA OE-YTHDF3-1
- GSM6631280 RNA OE-YTHDF3-1-Rep2 RNA OE-YTHDF3-1
- GSM6631281 RNA OE-YTHDF3-2-Rep1 RNA OE-YTHDF3-2
- GSM6631282 RNA OE-YTHDF3-2-Rep2 RNA OE-YTHDF3-2
- GSM6631283 RNA OE-YTHDF3-4-Rep1 RNA OE-YTHDF3-4
- GSM6631284 RNA OE-YTHDF3-4-Rep2 RNA OE-YTHDF3-4
- 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
- GSE182090 RNA-sequencing assay to Identify Genes Promoting Lung Metastasis of Esophageal Squamous Cell Carcinoma (ESCC) Cells 12 samples shares metastasis, promoting, rna-seq
- GSE289930 Proteogenomic Characterization of Primary Oral Cancer Unveils Extracellular Matrix Remodeling and Immunosuppressive Microenvironment Linked to Lymph Node Metastasis [RNA-seq] 33 samples shares metastasis, rna-seq
- GSE253036 Tumor Cell JAGGED-1 Promotes Lymph Node Metastasis and Predicts Recurrence in Lymph Node Positive Breast Cancer Patients 27 samples shares metastasis, 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.