Loss of 5-hydroxymethylcytosine is an epigenetic hallmark of melanoma
DNA methylation · human · 15 samples
- What it is
- DNA methylationChemical marks on DNA that help switch genes on or off.
- Organism
- Homo sapiens (human)
- Topic
- MelanomaThis series is part of our curated briefing on it.
- Samples
- 15 samples: 15 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 GSE38231_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 beta-value tables or raw IDAT files among the supplementary files.
Also filed as BioProject PRJNA167460 and SRA study SRP013379. 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 15 sample titles: 15 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.
- GSM937074 Input_Nevus_tissue
- GSM937075 Input_Melanoma_tissue
- GSM937076 Input_A2058 Mock cells
- GSM937077 Input_A2058 TET2 cells
- GSM937078 Input_A2058 TET2 M cells
- GSM937079 hMeDIP_Nevus_tissue
- GSM937080 hMeDIP_Melanoma_tissue
- GSM937081 hMeDIP_A2058 Mock cells
- GSM937082 hMeDIP_A2058 TET2 cells
- GSM937083 hMeDIP_A2058 TET2 M cells
- GSM937084 MeDIP_Nevus_tissue
- GSM937085 MeDIP_Melanoma_tissue
- GSM937086 MeDIP_A2058 Mock cells
- GSM937087 MeDIP_A2058 TET2 cells
- GSM937088 MeDIP_A2058 TET2 M cells
- GSE12391 Melanoma: comparison between common nevi, radial/vertical growth phase melanoma, metastases and dysplastic nevi 114 samples same disease briefing · shares melanoma
- GSE134459 Genome-wide maps of transcriptomic and epigenomic state in melanoma cell lines 73 samples same disease briefing · shares melanoma
- GSE230489 RNA-sequencing of cutaneous melanoma and non-small cell lung cancer biopsies 38 samples same disease briefing · shares melanoma
- GSE100797 Mutational and neoantigen load predict clinical benefit of adoptive T cell therapy in melanoma 25 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
- GSE142751 Genome-wide maps of chromatin state in 142 cancer cell lines [cell line] 855 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.