ALKBH5 facilitates the progression of skin cutaneous melanoma through promoting ABCA1 demethylation and inhibiting autophagy in an m6A-dependent manner
DNA methylation · human · 12 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
- 12 samples: 3 × A375 cells, shCtrl input vs 3 × A375 cells, shALKBH5 input vs 3 × A375 cells, shCtrl IP vs 3 × A375 cells, shALKBH5 IPGroups 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
- ALKBH5 facilitates the progression of skin cutaneous melanoma via mediating ABCA1 demethylation and modulating autophagy in an m(6)A-dependent mannerInternational journal of biological sciences · 2024
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 GSE253795_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 PRJNA1067136 and SRA study SRP484949. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 12 of them. 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.
- GSM8028024 A375 cells, shCtrl input 1 A375 cells, shCtrl input
- GSM8028025 A375 cells, shCtrl input 2 A375 cells, shCtrl input
- GSM8028026 A375 cells, shCtrl input 3 A375 cells, shCtrl input
- GSM8028027 A375 cells, shALKBH5 input 1 A375 cells, shALKBH5 in…
- GSM8028028 A375 cells, shALKBH5 input 2 A375 cells, shALKBH5 in…
- GSM8028029 A375 cells, shALKBH5 input 3 A375 cells, shALKBH5 in…
- GSM8028030 A375 cells, shCtrl IP 1 A375 cells, shCtrl IP
- GSM8028031 A375 cells, shCtrl IP 2 A375 cells, shCtrl IP
- GSM8028032 A375 cells, shCtrl IP 3 A375 cells, shCtrl IP
- GSM8028033 A375 cells, shALKBH5 IP 1 A375 cells, shALKBH5 IP
- GSM8028034 A375 cells, shALKBH5 IP 2 A375 cells, shALKBH5 IP
- GSM8028035 A375 cells, shALKBH5 IP 3 A375 cells, shALKBH5 IP
- GSE230489 RNA-sequencing of cutaneous melanoma and non-small cell lung cancer biopsies 38 samples same disease briefing · shares cutaneous
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- GSE317605 A Phase II Trial of Pembrolizumab plus Granulocyte Macrophage Colony Stimulating Factor in Advanced Biliary Cancer [CITE-Seq] 168 samples same disease briefing
- GSE12391 Melanoma: comparison between common nevi, radial/vertical growth phase melanoma, metastases and dysplastic nevi 114 samples same disease briefing
- GSE91061 Molecular portraits of tumor mutational and micro-environmental sculpting by immune checkpoint blockade therapy 109 samples same disease briefing
- GSE134459 Genome-wide maps of transcriptomic and epigenomic state in melanoma cell lines 73 samples same disease briefing
- GSE100797 Mutational and neoantigen load predict clinical benefit of adoptive T cell therapy in melanoma 25 samples same disease briefing
- 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
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.