Superior coverage for DNA methylation studies: fast and affordable
- Superior coverage– 4 million CpGs
- High throughput - 96 samples processed in one experiment
- Cost-efficient – Multiplex up to 6-8 samples/sequencing lane
- High efficiency and minimal bias - Low DNA degradation and reduced amplification
- Complete solution - Enzymatic digestion, library preparation, bisulfite conversion reagents, sequencing and bioinformatics
- Results provided within 8-10 weeks (standard project)
Examples of RRBS data generated with the Diagenode RRBS service using samples from four different species
| Species | No. of reads aligned (alignment rate) | No. of unique CpGs covered (alignment rate) | Bisulfite conversion rate (%) | Mean sequencing depth per covered CpG (×) |
|---|---|---|---|---|
| Human |
21,787,346 (74%) |
3,913,287 |
99.4 |
14 |
| Human FFPE |
27,290,117 (79%) |
2,525,053 |
99.7 |
28 |
| Rat |
27,499,313 (86%) |
1,663,104 |
99.0 |
38 |
| Dog |
14,053,009 (84%) |
3,572,384 |
99.4 |
9 |
| Zebrafish |
29,035,877 (83%) |
1,685,466 |
99.3 |
48 |
Standard analysis
Standard analysis |
File |
Description |
|
FastQ file QC |
Trimming report (.txt) |
contains statistics on read trimming |
|
Read filtering & trimming |
Alignment report (.txt) |
contains mapping statistics and methylation statistics of the reads |
|
BS-specific alignment |
Alignment file in BAM format (BAM) |
contains all the aligned reads, their positions on the genome and their methylation information, as per the standard SAM/BAM format |
|
C methylation extraction |
methylation extraction file (.cov) |
contains methylation information on all covered Cs, one line represents one C, each line has 6 fields: chromosome - start - end - methylation percentage - covering methylated reads - covering unmethylated reads. |
|
QC summary report |
bedGraph file formatted for UCSC browser (bedGraph) |
contains the same methylation information as the previous .cov file. It can be loaded into the UCSC Genome Browser or any similar viewer where the methylation information can be visualized. |
Comparative analysis
Genome-wide CpG methylation analysis |
Description |
|
Hierarchical clustering |
Clustering of samples according to DNA methylation level (without heatmap) |
|
Scatter plot + pearson correlation |
Correlations between the samples |
|
Histograms |
Distribution of DNA methylation levels and CpG coverage of each sample |
|
Principal Components Analysis |
Visualization of principle components that best explain the data |
|
Pie charts |
Distribution of covered CpGs across genomic and CpG regions |
Differentially methylated CpG analysis |
Description |
|
Hierarchical clustering and heatmap |
Clustering of DMRs with heatmap |
|
Csv file for DMRs |
DMRs identification |
|
Csv file for DMPs |
DMPs identification |
|
Bar chart |
DMPs repartition between hyper- and hypo-methylation for each chromosome |
|
Pie charts |
Distribution of DMPs across genomic and CpG regions |
