EZH2 reads DNA 6mA to regulate survival and drug resistance of human head and neck squamous carcinoma by suppressing RIOX2-CDKN1A-NRF2 signaling axis [MeDIP-ChIP-seq-shRNA]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 17 samples
- What it is
- ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
- Organism
- Homo sapiens (human)
- Topic
- Head and neck cancerThis series is part of our curated briefing on it.
- Samples
- 17 samples: 16 distinct titles, 1 of them repeatedGroups 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 GSE212437_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.
Also filed as BioProject PRJNA875427 and SRA study SRP395082. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 17 sample titles: 16 distinct titles with little repetition. 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.
- GSM6532802 ChIP-1-mock-EZH2
- GSM6532803 ChIP-1-mock-input
- GSM6532804 ChIP-1-shA1-3-EZH2
- GSM6532805 ChIP-1-shA1-3-input
- GSM6532806 ChIP-2-mock-EZH2
- GSM6532807 ChIP-2-mock-H3
- GSM6532808 ChIP-2-mock-input
- GSM6532809 ChIP-2-shA1-4-EZH2
- GSM6532810 ChIP-2-shA1-4-H3
- GSM6532811 ChIP-2-shA1-4-input
- GSM6532812 N6-mock-6mA-3
- GSM6532813 N6-mock-input-3
- GSM6532814 N6-shA1-3-6mA
- GSM6532815 N6-shA1-3-input
- GSM6532816 N6-mock-input
- GSM6532817 N6-shA1-4-6mA
- GSM6532818 N6-shA1-4-input
- GSE114446 Integrated single-cell and bulk gene expression and ATAC-seq reveals heterogeneity and early changes in pathways associated with resistance to cetuximab in HNSCC-sensitive cell lines 33 samples same disease briefing · shares resistance
- GSE176077 RNA-seq profiling of salivary transcriptome reveals potential diagnostic RNAs and oral microbial dysbiosis in oral squamous cell carcinoma 28 samples same disease briefing · shares squamous
- GSE140042 Single-cell atlas of head and neck squamous cell carcinoma 18 samples same disease briefing · shares squamous
- GSE185965 Single cell RNA sequencing of head and neck squamous carcinoma (HNSCC) patient sample 3 samples same disease briefing · shares squamous
- GSE173647 Single-cell Sequencing Analysis of Head and Neck Squamous Cell Carcinoma 2 samples same disease briefing · shares squamous
- GSE103322 Single cell RNA-seq analysis of head and neck cancer 5901 samples same disease briefing
- GSE139324 Immune landscape of viral- and carcinogen-drived head and neck cancer 63 samples same disease briefing
- GSE162738 Immune gene signatures in oropharyngeal cancers are associated with inverse prognosis by HPV-status 51 samples same disease briefing
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.