PHF19 drives PRC2 sub-nuclear compartmentalization to promote motility in TNBC cells [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)
- Topic
- Breast cancerThis series is part of our curated briefing on it.
- Samples
- 12 samples: 3 × 436_siNT vs 3 × 436_siPHF19 vs 3 × BoM_siNT vs 3 × BoM_siPHF19Groups 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 GSE291243_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 PRJNA1232645 and SRA study SRP568354. 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.
- GSM8831546 436_siNT_Rep1 436_siNT
- GSM8831547 436_siNT_Rep2 436_siNT
- GSM8831548 436_siNT_Rep3 436_siNT
- GSM8831549 436_siPHF19_Rep1 436_siPHF19
- GSM8831550 436_siPHF19_Rep2 436_siPHF19
- GSM8831551 436_siPHF19_Rep3 436_siPHF19
- GSM8831552 BoM_siNT_Rep1 BoM_siNT
- GSM8831553 BoM_siNT_Rep2 BoM_siNT
- GSM8831554 BoM_siNT_Rep3 BoM_siNT
- GSM8831555 BoM_siPHF19_Rep1 BoM_siPHF19
- GSM8831556 BoM_siPHF19_Rep2 BoM_siPHF19
- GSM8831557 BoM_siPHF19_Rep3 BoM_siPHF19
- 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
- GSE104675 Role for the Transcriptional Activator ZRF1 in Breast Cancer Progression and Endocrine Resistance 6 samples same disease briefing
- GSE10885 An integromic analysis reveals that metaplastic carcinomas are distinct from basal-like tumors. 244 samples same disease briefing
- GSE10886 A Supervised Risk Predictor of Breast Cancer Based on Biological Subtypes 226 samples same disease briefing
- GSE11121 The humoral immune system has a key prognostic impact in node-negative breast cancer 200 samples same disease briefing
- GSE291242 PHF19 drives PRC2 sub-nuclear compartmentalization to promote motility in TNBC cells [ChIP-seq] 24 samples shares phf19, prc2, tnbc, compartmentalization, sub-nuclear, motility, promote
- GSE118389 Unravelling subclonal heterogeneity and aggressive disease states in TNBC through single-cell RNA-seq [RNA-Seq] 1534 samples shares tnbc, rna-seq
- GSE277665 DOT1L and EZH2 cooperatively repress PRC2 targets to maintain the GC B cell identity in DLBCL [RNA-seq] 48 samples shares prc2, 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.