INVIEW MODIFICATION ANALYSIS

SKU#B10140818

Direct detection of different DNA base modifications with ultra-long reads

INVIEW MODIFICATION ANALYSIS is a sample-to-data service for unbiased detection of epigenetic marks on unamplified source material that requires no bisulfite treatment. The product simultaneously provides sequencing data and base-modification analysis from the same library. The service can identify a variety of DNA modifications in small genomes, without being limited to a certain type of epigenetic mark, such as 5-methylcytosine.

Highlights of INVIEW MODIFICATION ANALYSIS

  • Simultaneous detection of sequence and epigenetic variants
  • Resolve strand-specific modifications at single-base resolution
  • Discovery of unknown or unexpected modifications

Service required

Please select at least one of these options.

Pre-Sequencing

INVIEW MODIFICATION ANALYSIS

INVIEW MODIFICATION ANALYSIS

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ISO9001 Certification - GATC BiotechISO17025 Accreditation - GATC BiotechPacBio - Certified Service Provider

Product Details

Product Specifications

  • Library preparation with unamplified double-stranded input DNA
  • Identification of 5-methylcytosine (5mC), 4-methylcytosine (4mC), glucosylated 5-hydroxylmethylcytosine, 6-methyladenine (6-mA)
  • Detection of base modifications, single-nucleotide variants (SNVs) and InDels from one sequencing library
  • Unbiased base-modification analysis – no prior knowledge of modification needed
  • Includes final data report based on sound BioIT analysis
  • Extremely well suited for bacterial and small eukaryotic organisms

Accepted starting material for INVIEW MODIFICATION ANALYSIS:

  • 8 µg unamplified high-quality DNA (100 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 for INVIEW MODIFICATION ANALYSIS:

  • Pacific Biosciences

Bioinformatic analysis included in INVIEW MODIFICATION ANALYSIS:

  • Quality filtering of sequencing reads
  • Mapping against a reference sequence*)
  • Analysis of the polymerase kinetics during sequencing
  • Detection of potentially modified bases

*) Do you not have a reference sequence available? Combine INVIEW™ MODIFICATION ANALYSIS with INVIEW DE NOVO GENOME 2.0 to gain information on both DNA sequence and epigenetic modifications. See "Related Products" below.

Deliverables of INVIEW MODIFICATION ANALYSIS:

  • Filtered subreads (fasta)
  • Alignment file (bam)
  • Coverage report (bed)
  • Consensus sequence (fastq)
  • Table of detected modifications (csv, gff)

Delivery time depending on project size:

  • INVIEW Modification Analysis: genome size < 5 Mb
    • 30 days for up to 8 samples
    • 40 days for 9-24 samples
    • Express available:
      • 20 days for up to 8 samples
      • 30 days for 9-24 samples
  • INVIEW Modification Analysis: genome size 5.1 - 10 Mb
    • 35 days for up to 8 samples
    • 45 days for 9-24 samples
    • Express available:
      • 30 days for up to 8 samples
      • 35 days for 9-24 samples
  • INVIEW Modification Analysis: genome size 10.1 - 15 Mb
    • 35 days for up to 8 samples
    • 45 days for 9-24 samples
    • Express available:
      • 30 days for up to 8 samples
      • 35 days for 9-24 samples

Additional Information

INVIEW MODIFICATION ANALYSIS provides a bisulfite-independent approach for unbiased detection of DNA base modifications. The PacBio base-modification analysis is based on the kinetics of base incorporation, which are directly measured during the sequencing processes (Fig. 1). The kinetic signature of the polymerase allows users to perform a reliable and cost-effective analysis of the epigenetics of prokaryotes or small eukaryotes. The resulting data provide researchers with a deeper and more complete understanding of the regulation of biological processes and phenotypic variability of organisms.

Figure 1. The "GATC" sequence motif shown on the left-hand side of the graph indicates a N6-methyladenosine modification. The palindromic motif is modified on both strands, as can be seen by the increased interpulse duration ratios plotted above the A for the forward strand and below the T for the reverse strand. The second base-modified motif shown in this graph is non-palindromic and only modified in a single position on the forward strand. No base modification is detected on the reverse strand for this motif. The indicated interpulse duration ratios for each nucleotide of each strand are derived from dozens of reads and the same number of kinetic profiles. Some of the individual reads are shown at the bottom of the figure.

When seeking a deeper understanding of biological processes beyond the DNA code, studying base modifications is of great interest. If differences in the genetic code (DNA) cannot fully explain differences in function, analysing epigenetic profiles gives you deeper insight into the dynamic interactions between different levels of information (DNA, RNA, proteins).

Over 20 types of chemical base modifications are known to occur in nature. Studying this wide variety has traditionally been a challenge for scientists. Most studies to date have focused especially on cytosine methylation using indirect detection methods.
INVIEW™ Modification Analysis enables you to identify a wide variety of DNA base modifications in small genomes, without being limited to a certain type of modification.

Several modifications can be directly detected in unamplified source material, using single-molecule, real-time (SMRT®) sequencing:

  • 4-methylcytosine (4-mC)
  • 6-methyladenine (6-mA)
  • Glucosylated 5-hydroxymethylcytosine

Applications of INVIEW MODIFICATION ANALYSIS include:

  • Gene-expression studies
  • Research on regulation of metabolic pathways
  • Determination of microbial virulence
  • Characterisation of methyltransferase recognition motifs

FAQs

1. What kind of samples can be used?
The product is extremely well suited for genomic DNA isolated from prokaryotic or small eukaryotic organisms. No prior knowledge of the modifications in question is necessary.

2. Are other modifications than the ones mentioned detectable?
Additional detection of 5-methylcytosine and 5-hydroxymethylcytosine can be offered upon request. This type of base modification can be detected depending on the sequencing fold coverage per strand. Please contact us to define the appropriate coverage to meet the needs of your project.

3. Can I use DNA from whole-genome amplification (WGA) experiments as starting material?
Unamplified double-stranded input DNA is needed to perform base-modification analyses. Epigenetic information will be lost during PCR or other amplification methods, as the DNA polymerase does not incorporate the modifications into the newly synthesised strand.

4. Do I need to have a reference genome?
No. Analysis can be combined with our INVIEW DE NOVO GENOME service for simultaneous determination of the DNA sequence and epigenetic marks present in the genomes of organisms with no reference sequences. Both sequence and base modifications are analysed from a single DNA library.  

5. What kind of quality controls do you perform?
The quality and quantity of each incoming sample will be determined by appropriate methods upon receiving the sample and at various steps of the process.

6. 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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