Genome-wide maps of transcriptomic and epigenomic state in melanoma cell lines
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 18 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)
- Samples
- 18 samples: 18 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.
- Paper
- Sequential transcriptional waves and NF-κB-driven chromatin remodeling direct drug-induced dedifferentiation in cancerNature communications · 2026
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 GSE255263_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 PRJNA1074295 and SRA study SRP488677. 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 18 sample titles: 18 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.
- GSM8067755 M397_Day0_K27_H3K27ac_ChIPseq_rep2
- GSM8067756 M397_Day3_K27_H3K27ac_ChIPseq_rep2
- GSM8067757 M397_Day32_K27_H3K27ac_ChIPseq_rep2
- GSM8067758 M397_Drug_removal_K27_H3K27ac_ChIPseq_rep2
- GSM8067759 M397_Day0_K4_H3K4me3_ChIPseq_rep2
- GSM8067760 M397_Day3_K4_H3K4me3_ChIPseq_rep2
- GSM8067761 M397_Day32_K4_H3K4me3_ChIPseq_rep2
- GSM8067762 M397_Drug_removal_K4_H3K4me3_ChIPseq_rep2
- GSM8067763 M397_Day0_RelA_ChIPseq_rep1
- GSM8067764 M397_Day3_RelA_ChIPseq_rep2
- GSM8067765 HCC827_ctrl_RNA-seq
- GSM8067766 HCC827_D3_RNA-seq
- GSM8067767 HCC827_2W_RNA-seq
- GSM8067768 HCC827_3W_RNA-seq
- GSM8067769 HT29_ctrl_RNA-seq
- GSM8067770 HT29_D3_RNA-seq
- GSM8067771 HT29_2W_RNA-seq
- GSM8067772 HT29_3W_RNA-seq
- GSE142751 Genome-wide maps of chromatin state in 142 cancer cell lines [cell line] 855 samples shares genome-wide, state, lines, maps
- GSE329231 Epigenomic profiling of H3K9me3 and H3K27ac across melanoma cell lines with different mutational backgrounds 45 samples shares epigenomic, melanoma, lines
- GSE277165 Single-cell transcriptomics and epigenomics point to CD58/CD59-CD2 interactions in controlling primary melanoma growth and immunity 20 samples shares epigenomic, melanoma
- GSE309697 Generation of a Comprehensive Epigenomic Atlas in Clear Cell Renal Cell Carcinoma Informs Kidney Cancer Progression and Heritability 265 samples shares epigenomic
- GSE307670 Epigenetic reprogramming of stromal cell states underpins pathologic tissue niches in Crohn’s disease 148 samples shares state
- GSE245969 EP300/CREBBP acetyltransferase inhibition limits steroid receptor and FOXA1 signaling in prostate cancer cells 122 samples shares state
- GSE227974 MY-COMP, an inhibitor of the transcriptional activity of YAP-B-MYB, identifies NEK2 as a novel mediator of YAP oncogenesis in uveal melanoma cells 29 samples shares melanoma
- GSE324815 Intratumoral CD40 agonist sotigalimab in combination with pembrolizumab induces rapid activation of antigen presenting cells and drives anti-tumor responses in non-injected tumors in metastatic melanoma: Results of a phase 1/2 study 24 samples shares melanoma
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.