Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling [MethylationEPIC]
DNA methylation · human · 15 samples
- What it is
- DNA methylationChemical marks on DNA that help switch genes on or off.
- Organism
- Homo sapiens (human)
- Samples
- 15 samples: 5 × Guthrie T vs 2 × LNCaP vs 2 × PrECGroups 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.
Read the full summary ↓
Direct links to NCBI, 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.
Whole study · RAW.tar
Everything the authors deposited as one archive (GSE86831_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.
What the files usually look like: Look for beta-value tables or raw IDAT files among the supplementary files.
Also filed as BioProject PRJNA342658. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 9 samples.
How we read this: 3 replicated groups read from 15 sample titles; they account for 9 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.
- GSM2309170 LNCaP Rep1 LNCaP
- GSM2309171 LNCaP Rep2 LNCaP
- GSM2309172 PrEC Rep1 PrEC
- GSM2309173 PrEC Rep2 PrEC
- GSM2309174 CAF A
- GSM2309175 CAF B
- GSM2309176 CAF C
- GSM2309177 NAF A
- GSM2309178 NAF B
- GSM2309179 NAF C
- GSM2309180 Guthrie T-73 Guthrie T
- GSM2309181 Guthrie T-75 Guthrie T
- GSM2309182 Guthrie T-76 Guthrie T
- GSM2309183 Guthrie T-80 Guthrie T
- GSM2309184 Guthrie T-82 Guthrie T
- GSE93646 Microarray-based DNA methylation profiles of primary medulloblastomas 428 samples shares methylation, microarray
- GSE29505 Custom Illumina array DNA methylation analysis of 384 CpGs across five cancer types 290 samples shares methylation, illumina
- GSE65820 Whole genome characterisation of chemoresistant ovarian cancer [Illumina_450K_Methylation] 121 samples shares methylation, illumina
- GSE67751 Blood Illumina Inf 450 DNA methylation samples from HIV+ and HIV- human subjects 92 samples shares methylation, illumina
- GSE67749 Frontal lobe (brain) Illumina Inf 450 DNA methylation samples from HIV+ and HIV- human subjects 33 samples shares methylation, illumina
- GSE75073 Validation of a DNA methylation microarray for 850,000 CpG sites of the human genome enriched in enhancer sequences 7 samples shares methylation, microarray
- GSE74193 Mapping DNA methylation across development, genotype, and schizophrenia in the human frontal cortex 675 samples shares methylation
- GSE73801 DNA methylation data from CNS-PNETs and various other brain tumor samples 593 samples shares methylation
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.