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Methylation analysis of normal and tumor bile duct samples

GSE89803 Homo sapiens (human) DNA methylation 142 samples Submitted 2017/07/03 Platform GPL16304
At a glance

DNA methylation · human · 142 samples

What it is
DNA methylationChemical marks on DNA that help switch genes on or off.
Organism
Homo sapiens (human)
Samples
142 samples: 9 conditions, mostly with about 4 replicates eachGroups 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.
Summary (written by the submitters)
Genome wide DNA methylation profiling of normal and tumor bile duct samples. The Illumina HumanMethylation450 BeadChip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in 138 tumor bile duct samples and 4 normal bile duct samples.
This dataset
Open GSE89803 in finder → Find more human methylation datasets →
Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need.

All supplementary files ↗
3 · The original raw files

Whole study · RAW.tar

Everything the authors deposited as one archive (GSE89803_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.

Whole study · RAW.tar ↓

What the files usually look like: Look for beta-value tables or raw IDAT files among the supplementary files.

Also filed as BioProject PRJNA353360. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 28667006) ↗
Study design
9 conditions, mostly with about 4 replicates each
bileduct_tumor_methylation_CCA_TH ×51 bileduct_tumor_methylation_CCA_SG ×34 bileduct_tumor_methylation_CCA_RO ×21 bileduct_tumor_methylation_CCA_F ×16 bileduct_tumor_methylation_CCA_CH ×8 bileduct_tumor_methylation_CCA_IT ×4 bileduct_normal_methylation_NBD_SG ×4 bileduct_tumor_methylation_CCA_B ×2 +1 more

Supports a case/control comparison: 138 samples read as cases, 4 as controls.

How we read this: 9 replicated groups read from 142 sample titles; they account for 142 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.

Samples in this study

+ 102 more — browse all 142 samples with per-sample file links →

Datasets on a similar topic

Search all human methylation datasets in GEO →

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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.