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PacBio RS II

Single-molecule Real-time DNA sequencing system PacBio RS II provides detecting complementary DNA chain synthesis by a DNA-polymerase molecule at single-molecule level. This technology, based on marked fluorescent nucleotides and high resolution confocal microscopy, allows real-time sequencing by many polymerases simultaneously. The main advantage of the SMRT, or single molecule real time sequencing technology is its huge read length: on average it comes to 4000 bp, although several reads can reach up to 30 000 bp.

Application examples:

  • De novo genomes sequencing (including complex ones)
  • Hybrid sequencing of genomes (in cooperation with Illumina)
  • Extensive genome variations detection
  • Methylation analysis
  • RNA sequencing

Sequencing services:

Average read length Data per SMRT Cell Number of reads Run time Price per SMRT Cell
3000-4000 bp 300-400Mb ~55 000 4-12 weeks Request a quote

Library preparation services:

Library type Run time Price per sample
DNA-library (10Kb) 2-6 weeks Request a quote
DNA-library (20Kb) 4-6 weeks Request a quote
RNA-library 4-12 weeks Request a quote
Ask question | Request a quote

Purified DNA:

  • total amount — not less than 5 ug
  • concentration — not less than 100 ng/ul
  • average fragment length over 20 000 bp, no smear
  • OD260/280=1.8-2.0
  • no RNA contamination

Purified RNA:

  • total amount — not less than 5 ug
  • concentration — not less than 100 ng/ul
  • 28S:18S RNA ≥ 1.0, RIN ≥ 7.0
  • OD260/280=1.8-2.0, OD260/230 ≥ 2.0

Lab services:

  • Biomaterial-based DNA extraction
  • Biomaterial-based RNA extraction
  • Single-cell sequencing
  • Target DNA fragments enrichment
  • mRNA enrichment
  • Repeated sample quality control
  • RNase treatment
  • Gaps filled by Sanger sequencing

Additional Data Analysis:

Basic bioinformatics services:
  • Sequencing quality and coverage uniformity analysis
  • Data filtering (adapters and low-quality reads removal)
  • De novo assembling
  • Reference reads mapping
  • Data phasing
  • GC-compound analysis
Genomic data assays:
  • SNV search and annotation (single-nucleotide variations)
  • Somatic SNV search and annotation (single-nucleotide variations)
  • InDel (insertions and deletions) search and annotation
  • CNV search and annotation (copy number variations)
  • ncRNA search and annotation
  • Comparative genomic analysis
  • KEGG, Swissprot, GO, Nr and COG genes search and annotation
  • Gene families identification (for animals: TreeFam, for plants: OrthoMCL)
  • Association analysis: genotype-phonotype, haplotype-phenotype and genes interactions research
  • Species divergence time evaluation
  • Genetic maps constructing
  • LD (Linkage disequilibrium) analysis
  • Phylogenetic analysis
  • Principal component analysis (PCA)
  • QTL mapping
RNA data analysis:
  • Gene expression arrays (qualitative)
  • Gene expression arrays (quantitative)
  • New transcripts forecasting and annotation
  • miRNA, rRNA, tRNA, snRNA, etc. search by mapping in miRBase, Rfam и Genbank
  • New miRNAs and their secondary structures forecasting in Mireap
  • CDS forecasting
  • Search of transcripts, formed as a result of alternative splicing
  • Unigene GO classification
  • Metabolic pathways analysis
  • Differential expression analysis (for 2 and more samples)
  • General and specific transcripts search (for 2 and more samples)
  • Principal component analysis (PCA) (for 5 and more samples)
Methylation analysis:
  • Methylation level calculation (individual sample)
  • Promoters and CpG-islands coverage analysis
  • Identification of deferentially methylated regions (for 2 and more samples)
Metagenomic analysis:
  • Qualitative and quantitative analysis of species representation per sample
  • Reads mapping on bacterial, viral, fungal and archaeal genomes analysis

Selected publications:

  • Chin, C. S., Alexander, D. H., Marks, P., Klammer, A. A., Drake, J., et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nature methods. 2013. V. 10. P. 563-9.
  • 2Koren, S., Schatz, M. C., Walenz, B. P., Martin, J., Howard, J. T., et al. Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nature biotechnology. 2012. V. 30. P. 693-700.
  • Huddleston, J., Ranade, S., Malig, M., Antonacci, F., Chaisson, M., et al. Reconstructing complex regions of genomes using long-read sequencing technology. Genome research. 2014. V. 24. P. 688-96.
  • Fang, G., Munera, D., Friedman, D. I., Mandlik, A., Chao, M. C., et al. Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing. Nature biotechnology. 2012. V. 30. P. 1232-9.
  • Zhang, W., Ciclitira, P. & Messing, J. PacBio sequencing of gene families - a case study with wheat gluten genes. Gene. 2014. V. 533. P. 541-6.
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