Epigenetics & Chromatin Analysis

Methylation arrays, bisulfite sequencing, ChIP-Seq, ATAC-Seq and CUT&Tag — processed, tested and interpreted against the right background model.

Epigenomic data carries more technical structure than most data types: bisulfite conversion efficiency, probe cross-reactivity on arrays, fragment size distribution in ATAC-Seq, and background in ChIP all shape the result before any biology is measured.

We check each of those explicitly and report them, because a differentially methylated region that turns out to track a batch is worse than no result at all.

Data We Accept

Illumina methylation array IDAT files (450K, EPIC, EPICv2)
Whole genome or reduced representation bisulfite sequencing FASTQ
ChIP-Seq, CUT&RUN or CUT&Tag FASTQ with matched input or IgG
ATAC-Seq or scATAC-Seq FASTQ files
Sample sheets with batch, chip position and cell composition information

Questions We Answer

Which regions are differentially methylated between my groups?
Where does my transcription factor bind, and does that change with treatment?
Which regions become accessible during differentiation or disease?
Which motifs are enriched in my peak set?
Is my methylation signal confounded by cell composition?

What We Do

Each project uses the subset of these that your research question requires.

Methylation Array Analysis

Normalisation, probe filtering, cell type deconvolution, and differential methylation at probe and region level with minfi, limma and DMRcate.

Bisulfite Sequencing

Alignment with Bismark, conversion efficiency assessment, coverage filtering and differential methylation calling at CpG and region level.

ChIP-Seq, CUT&RUN and CUT&Tag

Alignment, quality metrics including FRiP and cross-correlation, peak calling against matched controls, and differential binding analysis across conditions.

ATAC-Seq

Fragment size assessment, mitochondrial read removal, peak calling, differential accessibility, and footprinting where coverage permits.

Annotation and Motif Analysis

Peak and region annotation to genomic features, motif enrichment with HOMER or MEME, and integration with expression data where you have it.

Epigenetic Clocks

Age acceleration estimates from methylation data using established clock models, with the caveats about non-European populations stated clearly.

What You Receive

Differentially methylated positions and regions with annotation
Peak sets in BED and narrowPeak format with QC metrics
Differential binding or accessibility results
Motif enrichment tables and genome browser tracks
Cell composition estimates where relevant
Full processing code and reference versions

Tools We Use

minfi, limma, DMRcate, sesame
Bismark, MethylDackel, methylKit
Bowtie2, MACS3, SEACR
DiffBind, csaw, DESeq2
HOMER, MEME Suite, ChIPseeker
deepTools, IGV tracks

Typical turnaround: 3–5 weeks depending on data type and sample number

Indicative price: From $799 for a methylation array study through to differential methylation

Reduced rates are available for students and researchers at African public institutions. Every project is quoted in writing before work begins.

Epigenetics & Chromatin Analysis

Data We Accept

Questions We Answer

What We Do

Methylation Array Analysis

Bisulfite Sequencing

ChIP-Seq, CUT&RUN and CUT&Tag

ATAC-Seq

Annotation and Motif Analysis

Epigenetic Clocks

What You Receive

Tools We Use

Tell us about your data and we will scope it — free, within one working day.

+233 558 017 827

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