INVIEW EPIGENOME RRBS-SEQ

SKU#B10140828

Cost-efficient analysis of methylated regions in mammals

INVIEW EPIGENOME RRBS-Seq is a standardised, reduced representation bisulfite sequencing (RRBS-Seq) service which offers targeted genome-wide analysis of high CG-content areas of the genome. The bisulfite-based service offers next-generation sequencing (NGS) of CpG-rich DNA fragments and professional Bio-IT analysis to generate a comprehensive data report valuable to any epigeneticist interested in mammalian cytosine methylation.

Highlights of INVIEW EPIGENOME RRBS-Seq:

  • Highly efficient enrichment of genomic regions with high CpG content
  • Fewer reads necessary for a maximum amount of data
  • Economical analysis of epigenetic changes on a genome-wide scale

Service required

INVIEW EPIGENOME RRBS-SEQ incl. 50 million read pairs (2 x 50 bp)

Additional data output

Pre-Sequencing

Bioinformatic analysis

INVIEW EPIGENOME RRBS-SEQ

INVIEW EPIGENOME RRBS-SEQ

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Product Details

Product Details

Complete service provided by INVIEW EPIGENOME RRBS-Seq including:

  • Superior capture of CpG rich regions of the genome
  • Established protocols for low-input DNA
  • Optimised bisulfite treatment and library preparation
  • Expert Bio-IT analysis
  • Streamlined workflows under diagnostic conditions
  • Extremely well suited for mammals
  • Depending on the coverage needed, additional RRBS data packages of 5 GB per sample can be ordered without impacting the delivery time

Accepted starting material for INVIEW EPIGENOME RRBS-Seq

  • 2 µg unamplified high quality DNA (20 ng/µL)
  • DNA isolation available as additional service for tissue samples and cells

Please note that only S1-classified material is accepted for DNA isolation ordered online. More information about the current rules for classifying biological material can be found here. Please contact us for further information on isolating DNA from material classified as S2.

Sequencing platform used for INVIEW EPIGENOME RRBS-Seq

  • Illumina

Sequencing mode

  • 50 bp paired-end reads

Bioinformatic analysis included in INVIEW EPIGENOME RRBS-Seq

  • Applicable to human, mouse or rat; other organisms possible upon request
  • Assessment of sequence quality and filtering
  • Mapping of sequences against genomic reference and refinement of data
  • SNP detection and annotation of variants
  • Methylation profiling including annotation of methylated sites
  • Comprehensive Data Analysis Report

Deliverables of INVIEW EPIGENOME RRBS-Seq – Non-comparative mode

Genome alignment

  • Binary alignment map (BAM)
  • Indexed BAM

Methylation report

  • Methylation rates (tsv)
  • Coverage and Methylation plots (png)
  • CpG methylation table including annotated variants and effects (vcf|tsv)

Variants – SNPs

  • Variant Call Format (vcf)
  • Tab Separated table (tsv)

Deliverables of INVIEW EPIGENOME RRBS-Seq –Comparative mode
(starting with 2 groups)

Genome alignment

  • Binary alignment map (BAM)
  • Indexed BAM

Methylation report  

  • Methylation rates (tsv)
  • Coverage and Methylation plots (png)
  • CpG methylation table (vcf|tsv)

Variants – SNPs

  • Variant Call Format (vcf)
  • Tab Separated table (tsv)

Differential Methylation Analysis

  • Correlation plots (png)
  • Annotation plots (png)
  • Hyper- and hypomethylated regions (tsv)

Delivery time

  • 25 days for up to 8 samples; more than 8 samples upon request

Additional Information

INVIEW EPIGENOME RRBS-Seq is a cost-effective alternative to whole-genome bisulfite sequencing. The full-service package offers targeted, genome-wide analysis of the methylation status of all nucleotides across mammalian genomes. Since GC-rich areas are believed to be the main carriers of cytosine methylation in mammals, the bisulfite-based method focuses on genomic regions with high GC content. Before RRBS library preparation, the CpG sites are efficiently enriched, maximising the amount of methylation data that can be retrieved from a relatively small amount of sequencing reads. The method is advantageous for the characterisation of repeated sequences and for samples with low-input DNA.

Specific applications of RRBS-Seq:

  • Identification and analysis of differentially methylated regions between samples
  • Epigenetic cancer profiling
  • Analysis of methylation levels during development, cellular differentiation
  • Tissue-specific epigenetic differences
  • Biomarker discovery

FAQs

1. What is the difference between BS-Seq and RRBS-Seq?
BS-Seq offers whole-genome bisulfite sequencing, whereas RRBS-Seq provides targeted bisulfite sequencing. BS-Seq is applicable to nearly any organism of interest and provides superior genome-wide coverage, including coverage of regions of poorly assembled, non-coding DNA. RRBS-Seq is generally used for mammalian organisms such as humans and mice. The technique offers high mapping efficiency and increases sequencing depth without increasing the amount of required NGS.

2. Can I use RRBS-Seq to study any organism?
RRBS-Seq can be used for any type of cell tissue from mammalian organisms. It is beneficial for low-input DNA samples, including formalin-fixed paraffin embedded (FFPE) samples.

3. Where do I obtain my results?
All raw and analysed data can be downloaded via your secure myGATC online account. A demo data report for a typical RRBS-Seq project can be viewed after login.

4. What coverage should I use?
Sequencing results can vary depending on the composition of the analysed genome and the mammalian organism sequenced. Typically, 1x to 5x sequencing coverage of the “original” genome is recommended.

5. What starting material should I send and how much of it?
For sequencing on the Illumina platform, we require 2 µg of high-quality DNA that has not been amplified or bisulfite treated.

6. Do you guarantee a certain output?
We guarantee 50 million read pairs (+/- 10%) with 5 Gb raw data output (+/- 10%) per package.
 
7. What kind of quality controls do you perform?
The quality and quantity of each incoming sample will be determined by appropriate methods. Further quality controls are performed at various steps of the process.

8. Where should I send my samples?
Please post your samples to:
GATC Biotech AG
European Genome and Diagnostics Centre
Jakob-Stadler-Platz 7
78467 Konstanz
Germany
 
Please do not use GATC Collection Points for shipping NextGen samples, because this will delay sample arrival at the appropriate destination!

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