Epigenetic Profiling Reveals Key Super-Enhancer Networks Driving Oncogenesis in HPV-Positive HNSCC
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)
- Samples
- 12 samples: 3 × O47, DMSO, vs 3 × O47, JQ1, vs 3 × O90, DMSO, vs 3 × O90, JQ1,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.
- Paper
- Epigenetic profiling reveals key super-enhancer networks driving oncogenesis in HPV-positive HNSCCiScience · 2025
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 GSE281308_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 PRJNA1183355 and SRA study SRP543811. 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.
- GSM8618497 O47, DMSO, rep1 O47, DMSO,
- GSM8618498 O47, DMSO, rep2 O47, DMSO,
- GSM8618499 O47, DMSO, rep3 O47, DMSO,
- GSM8618500 O47, JQ1, rep1 O47, JQ1,
- GSM8618501 O47, JQ1, rep2 O47, JQ1,
- GSM8618502 O47, JQ1, rep3 O47, JQ1,
- GSM8618503 O90, DMSO, rep1 O90, DMSO,
- GSM8618504 O90, DMSO, rep2 O90, DMSO,
- GSM8618505 O90, DMSO, rep3 O90, DMSO,
- GSM8618506 O90, JQ1, rep1 O90, JQ1,
- GSM8618507 O90, JQ1, rep2 O90, JQ1,
- GSM8618508 O90, JQ1, rep3 O90, JQ1,
- GSE268227 Enhancer-promoter hubs organize transcriptional networks promoting oncogenesis and drug resistance (RNA-Seq) 6 samples shares oncogenesis, networks
- GSE268228 Enhancer-promoter hubs organize transcriptional networks promoting oncogenesis and drug resistance 18 samples shares oncogenesis, networks
- GSE274408 Heat Shock Transcription Factor 1 Facilitates Liver Cancer Progression by Driving Super-Enhancer-Mediated Transcription of MYCN 12 samples shares super-enhancer, driving
- GSE270047 Analytical performance of OncoPrism-HNSCC, an RNA-based assay to inform immune checkpoint inhibitor treatment decisions for recurrent/metastatic head and neck squamous cell carcinoma 434 samples shares hnscc
- GSE235223 Transcriptional characterization of adjuvantly radio(chemo)therapy treated head and neck squamous cell carcinoma (HNSCC). 134 samples shares hnscc
- GSE237454 Gene regulation profiling by KMT2D under different glucose conditions in HNSCC (RNAseq) 14 samples shares hnscc
- GSE286234 Bulk RNA-seq profiling of human head and neck squamous cell carcinoma (HNSCC) with primary tumors and metastatic lymph nodes 10 samples shares hnscc
- GSE173855 Transcriptomic characterization of paired primary and recurrent HNSCC tumors 68 samples shares hnscc
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.