Epigenomic profiling of H3K9me3 and H3K27ac across melanoma cell lines with different mutational backgrounds
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 45 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
- MelanomaThis series is part of our curated briefing on it.
- Samples
- 45 samples: 45 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.
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 GSE329231_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 PRJNA1458169 and SRA study SRP695286. 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 45 sample titles: 45 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.
- GSM9699679 SK-Mel-19, replicate 1 (Input)
- GSM9699680 SK-Mel-19, replicate 2 (Input)
- GSM9699681 SK-Mel-19, replicate 3 (Input)
- GSM9699682 SK-Mel-19, H3K9me3, replicate 1 (ChIP)
- GSM9699683 SK-Mel-19, H3K9me3, replicate 2 (ChIP)
- GSM9699684 SK-Mel-19, H3K9me3, replicate 3 (ChIP)
- GSM9699685 SK-Mel-19, H3K27ac, replicate 1 (ChIP)
- GSM9699686 SK-Mel-19, H3K27ac, replicate 2 (ChIP)
- GSM9699687 SK-Mel-19, H3K27ac, replicate 3 (ChIP)
- GSM9699688 SK-Mel-28, replicate 1 (Input)
- GSM9699689 SK-Mel-28, replicate 2 (Input)
- GSM9699690 SK-Mel-28, replicate 3 (Input)
- GSM9699691 SK-Mel-28, H3K9me3, replicate 1 (ChIP)
- GSM9699692 SK-Mel-28, H3K9me3, replicate 2 (ChIP)
- GSM9699693 SK-Mel-28, H3K9me3, replicate 3 (ChIP)
- GSM9699694 SK-Mel-28, H3K27ac, replicate 1 (ChIP)
- GSM9699695 SK-Mel-28, H3K27ac, replicate 2 (ChIP)
- GSM9699696 SK-Mel-28, H3K27ac, replicate 3 (ChIP)
- GSM9699697 UACC-62, replicate 1 (Input)
- GSM9699698 UACC-62, replicate 2 (Input)
- GSM9699699 UACC-62, replicate 3 (Input)
- GSM9699700 UACC-62, H3K9me3, replicate 1 (ChIP)
- GSM9699701 UACC-62, H3K9me3, replicate 2 (ChIP)
- GSM9699702 UACC-62, H3K9me3, replicate 3 (ChIP)
- GSM9699703 UACC-62, H3K27ac, replicate 1 (ChIP)
- GSM9699704 UACC-62, H3K27ac, replicate 2 (ChIP)
- GSM9699705 UACC-62, H3K27ac, replicate 3 (ChIP)
- GSM9699706 SK-Mel-103, replicate 1 (Input)
- GSM9699707 SK-Mel-103, replicate 2 (Input)
- GSM9699708 SK-Mel-103, replicate 3 (Input)
- GSM9699709 SK-Mel-103, H3K9me3, replicate 1 (ChIP)
- GSM9699710 SK-Mel-103, H3K9me3, replicate 2 (ChIP)
- GSM9699711 SK-Mel-103, H3K9me3, replicate 3 (ChIP)
- GSM9699712 SK-Mel-103, H3K27ac, replicate 1 (ChIP)
- GSM9699713 SK-Mel-103, H3K27ac, replicate 2 (ChIP)
- GSM9699714 SK-Mel-103, H3K27ac, replicate 3 (ChIP)
- GSM9699715 UACC-257, replicate 1 (Input)
- GSM9699716 UACC-257, replicate 2 (Input)
- GSM9699717 UACC-257, replicate 3 (Input)
- GSM9699718 UACC-257, H3K9me3, replicate 1 (ChIP)
+ 5 more — browse all 45 samples with per-sample file links →
- GSE134459 Genome-wide maps of transcriptomic and epigenomic state in melanoma cell lines 73 samples same disease briefing · shares epigenomic, melanoma
- GSE100797 Mutational and neoantigen load predict clinical benefit of adoptive T cell therapy in melanoma 25 samples same disease briefing · shares mutational, melanoma
- GSE12391 Melanoma: comparison between common nevi, radial/vertical growth phase melanoma, metastases and dysplastic nevi 114 samples same disease briefing · shares melanoma
- GSE91061 Molecular portraits of tumor mutational and micro-environmental sculpting by immune checkpoint blockade therapy 109 samples same disease briefing · shares mutational
- GSE230489 RNA-sequencing of cutaneous melanoma and non-small cell lung cancer biopsies 38 samples same disease briefing · shares melanoma
- GSE123728 Clinical and Immunologic Activity of a Single Dose of Neoadjuvant PD-1 Blockade and Predictors of Clinical Outcomes in Resectable Melanoma 24 samples same disease briefing · shares melanoma
- GSE130956 Investigation of ST8SIA1 expression in icaritin-treated and untreated melanoma cell lines 12 samples same disease briefing · shares melanoma
- GSE140150 A rare subpopulation of melanoma cells with low expression of metastasis suppressor NME1 has a neural crest-like phenotype and is highly metastatic in vivo 6 samples same disease briefing · 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.