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HiSeq 2000/2500

Powerful and efficient sequencing platforms Illumina HiSeq 2000 and HiSeq 2500 allow carrying out large-scale projects of genome, exome and transcriptome sequencing and many others. These systems are able to analyze 1-2 flow cells, 8 lanes each. Read length varies from 50 to 250 bp (for HiSeq 2500 in Rapid-Run mode), which are either pair-end, or single reads. By sample multiplexing one can reach up to 192 samples per lane to achieve the combination of affordable price and large numbers of analyzed samples.

Examples of application:

Whole-genome sequencing, targeted resequencing, gene expression level detection, DNA methylation profiling, de novo sequencing, metagenomic studies, ChiP-seq.

Sequencing services:

Read length Output data Run time Price
2 x 100 bp~ 30Gb (1 lane) 3-6 weeksRequest a quote
2 x 100 bp~ 15Gb 6-12 weeksRequest a quote
2 x 100 bp~ 10Gb 6-12 weeksRequest a quote
2 x 100 bp~ 5Gb 6-12 weeksRequest a quote
2 x 100 bp~ 3Gb 6-12 weeksRequest a quote
2 x 100 bp~ 1Gb 6-12 weeksRequest a quote
1 x 100 bp~ 15Gb (1 lane) 3-6 weeksRequest a quote
1 х 50 bp~ 15Gb (1 lane) 3-6 weeksRequest a quote

Library prepatation services:

Library type Run time Price
DNA-library (PCR-free) 1-3 weeks Request a quote
RNA-library 1-4 weeks Request a quote
Mate-pair library (up to 20Kb)) 4-12 weeks Request a quote
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Purified DNA:

total amount – not less than 3 ug, concentration – not less than 50 ng/ul, average fragment length – over 10,000 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 50 ng/ul, 28S:18S RNA ≥ 1.0, RIN ≥ 7.0, OD260/280 = 1.8-2.0, OD260/230 ≥ 2.0.

Prepared libraries:

total amount – not less than 50 ng, concentration – not less than 5 ng/ul, insert length — 200-1000 bp, the libraries are prepared using reagents compatible with TruSeq Illumina (production of Illumina, NEB, etc). The decline in the requirements to the DNA/RNA amounts and concentrations is possible, when using library preparation kits, based on amplification.

Additional lab services:

Biomaterial-based DNA extraction, biomaterial-based RNA extraction, whole-genome amplification (in case of biomaterial lack), single-cell sequencing, target DNA fragments enrichment, mRNA enrichment, repeated sample quality control, RNase treatment, gaps filled by Sanger sequencing.

Additional data services:

Basic bioinformatic services: sequencing quality and coverage uniformity tests, 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: qualitative genes expression analysis, 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 detection, promoters and CpG-islands coverage analysis, identification of deferentially methylated regions (for 2 and more samples). Metagenomic analysis: qualitative and quantitative analysis of species per sample, reads mapping on bacterial, viral, fungal and archaeal genomes analysis.

Selected publications:

  • Lam et al. Performance comparison of whole-genome sequencing platforms. Nat Biotechnol. 2011 Dec 18;30(1):78-82.
  • Hashimshony et al. Spatiotemporal transcriptomics reveals the evolutionary history of the endoderm germ layer. Nature. 2015 Mar 12;519(7542):219-22.
  • Smallwood et al. Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity. Nat Methods. 2014 Aug;11(8):817-20.
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