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Glycation DNA immunoprecipitation sequencing (GlyDIP-seq) for detecting epigenetic effects unique to diabetes

GSE296615 Homo sapiens (human) RNA-seq (gene expression) 10 samples Submitted 2026/05/18 Platform GPL34281
At a glance

RNA-seq (gene expression) · human · 10 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Homo sapiens (human)
Samples
10 samples: 3 × hNPC(AG09429), PBS treatment, 24h, vs 3 × hNPC(AG09429), MG treatment, 24h, vs 2 × hNPC(GM03440), PBS treatment, 24h, vs 2 × hNPC(GM03440), MG treatment, 24h,Groups 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.
Summary (written by the submitters)
DNA glycation, a non-enzymatic modification triggered by reactive metabolites such as methylglyoxal (MG), has been implicated in various metabolic and neurological disorders. However, its genome-wide distribution and biological consequences in the developing brain remain largely unexplored. To address this gap, we developed a novel method, GlyDIP-seq, which enables high-resolution profiling of glycation-derived DNA lesions (specifically N²-carboxyethyl-2'-deoxyguanosine, CEdG) across the genome.
This dataset
Open GSE296615 in finder → Find more human RNA-seq datasets →
Download · which file do I need?

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.

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, or the whole study as GSE296615_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

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.

Raw reads on ENA ↗

What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1260240 and SRA study SRP583798. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
3 × hNPC(AG09429), PBS treatment, 24h, vs 3 × hNPC(AG09429), MG treatment, 24h, vs 2 × hNPC(GM03440), PBS treatment, 24h, vs 2 × hNPC(GM03440), MG treatment, 24h,

Supports a between-group comparison across 10 samples.

How we read this: 4 replicated groups read from 10 sample titles; they account for 10 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
Datasets on a similar topic

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