Genome-wide mapping of human H4K20me3 in the HN-SCC-151 HPV-negative head and neck squamous cell carcinoma cells treated with DMSO or the SUV420H1 inhibitor A-196/siNC (control) or siSUV420H1 siRNAs.
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 24 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
- 24 samples: 24 samples, each with a distinct title — no replicated groupsGroups 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 GSE333738_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 PRJNA1472477 and SRA study SRP704787. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 24 sample titles: 24 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.
- GSM9771977 VS999_SCC151_DMSO_IgG_rep1
- GSM9771978 VS1000_SCC151_DMSO_H3K4me3_rep1
- GSM9771979 VS1001_SCC151_DMSO_H3K4me3_rep2
- GSM9771980 VS1002_SCC151_DMSO_H3K27me3_rep1
- GSM9771981 VS1003_SCC151_DMSO_H3K27me3_rep2
- GSM9771982 VS1004_SCC151_DMSO_H4K20me3_rep1
- GSM9771983 VS1005_SCC151_DMSO_H4K20me3_rep2
- GSM9771984 VS1006_SCC151_DMSO_H4K20me3_rep3
- GSM9771985 VS1010_SCC151_A-196_H4K20me3_rep1
- GSM9771986 VS1011_SCC151_A-196_H4K20me3_rep2
- GSM9771987 VS1012_SCC151_A-196_H4K20me3_rep3
- GSM9771988 VS1030_SCC151_IgG_rep1
- GSM9771989 VS1032_SCC151_H3K4me3_rep1
- GSM9771990 VS1033_SCC151_H3K4me3_rep2
- GSM9771991 VS1034_SCC151_H3K27me3_rep1
- GSM9771992 VS1035_SCC151_H3K27me3_rep2
- GSM9771993 VS1036_SCC151_siNC_H4K20me3_rep1
- GSM9771994 VS1037_SCC151_siNC_H4K20me3_rep2
- GSM9771995 VS1038_SCC151_siNC_H4K20me3_rep3
- GSM9771996 VS1039_SCC151_siNC_H4K20me3_rep4
- GSM9771997 VS1040_SCC151_siSUV420H1_H4K20me3_rep1
- GSM9771998 VS1041_SCC151_siSUV420H1_H4K20me3_rep2
- GSM9771999 VS1042_SCC151_siSUV420H1_H4K20me3_rep3
- GSM9772000 VS1043_SCC151_siSUV420H1_H4K20me3_rep4
- 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
- GSE164690 Investigating Immune and Non-Immune Cell Interactions in Head and Neck Tumors by Single-Cell RNA Sequencing 51 samples same disease briefing
- GSE181919 Single-cell transcriptome profiling of the stepwise progression of head and neck cancer 37 samples same disease briefing
- 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
- GSE172146 Aberrant translation regulation by METTL1/WDR4-mediated tRNA N7-methylguanosine modification drives HNSCC progression 28 samples same disease briefing
- 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
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.