Instrumentation


Next generation sequencing

Illumina HiSeq3000

  • sequencing-by-synthesis: detection of single bases being incorporated into growing DNA strand
  • 1 × 150 bp reads/2 × 150 bp reads
  • 1 × 100 bp reads/2 × 100 bp reads
  • 2 × 75 bp reads
  • 1 × 50 bp reads
  • up to 750 Gbases per run
  • many applications, e.g. de novo genome sequencing, genome re-sequencing, transcriptome sequencing (RNA-Seq), ChIP sequencing, small RNA sequencing, bisulfite sequencing, …

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Illumina HiSeq2500

  • sequencing-by-synthesis: detection of single bases being incorporated into growing DNA strand
  • 2 × 250 bp reads in Rapid mode
  • 1 × 50 bp reads
  • up to 280 Gbases per run in Rapid mode
  • many applications, e.g. de novo genome sequencing, genome re-sequencing, transcriptome sequencing (RNA-Seq), ChIP sequencing, bisulfite sequencing, …

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10x Genomics Chromium Controller – available since spring 2017

  • a droplet-based system to
    a) label large DNA fragments (> 50 kb) with one barcode per fragment to create linked reads
    b) label single cells from a population of cells individually to facilitate high throughput single cell sequencing
  • optimal for large, diploid genomes (> 800 Mb)
  • low DNA input amount (1 ng/run) for the genome chip
  • creates long distance genome information from short Illumina reads
  • many applications, e.g. whole genome (de novo) sequencing, haplotype determination, improving of genome drafts, SNP phasing, …

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Pacific Biosciences Sequel – available since spring 2017

  • the successor of the RSII, with higher output per SMRTCell at comparable read length
  • single-molecule sequencing
  • sequencing of very long reads (10 -15 kb)
  • many applications, e.g. de novo genome sequencing, genome finishing, base modification analysis, full length cDNA sequencing, transcript isoform sequencing, …

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Capillary electrophoresis systems

Agilent 2100 Bioanalyzer

  • quality control and quantification of DNA and RNA samples
  • lab-on-a-Chip analysis with preformatted chips (10-12 samples/chip)

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Agilent 2200 TapeStation

  • quality control and quantification of DNA and RNA samples
  • fast and scalable analysis up to 96 samples at the time

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Caliper GX

  • high throughput quality control and quantification of DNA and RNA samples
  • analysis directly from 96 or 384 plates
  • PCR based genotyping

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Advanced analytical femtoPulse

  • extremely low detection limit – can detect DNA and RNA in fg amounts
  • scalable analysis with broad range of RNA and DNA detection methods
  • “pulse field” function with very good resolution at high molecular weight DNA ranges (> 165 kb)

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Robotics


Caliper Sciclone G3

Robotics unit I: Caliper sciclone G3

  • operating in 96-well dimension
  • applications: DNA and RNA library preparation

Robotics unit II: Thermo Scientific F5 Robot

  • connected to several other instruments (Beckman Coulter Biomek NXp 384 and Biomek FX 96, fridge, carousel, centrifuges…)
  • applications: PCR product purification and DNA preparation from plasmids, fosmids, BACs

Robotics unit III: Tecan EVO

  • applications: 8-, 96- or 384-channel liquid handling

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Others

ABI ViiA7 Real-Time PCR System

  • applications: qPCR, Standard curve, Comparative Ct, Genotyping, Presence/Absence
  • run time: ~35 min for 384-well, using ABI Fast Master Mix

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Covaris S2

  • fragmentation of nucleic acids via sonication

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BluePippin

  • targeted size selection of DNA Fragments from 90 bp to 50kb
  • up to 5 samples at the same time
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SageELF

  • collection of up to 12 contiguous fractions from a single DNA sample
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BioRad CHEF-DR III

  • pulsed field electrophoresis system
  • high resolution separation of high molecular weight DNA (200 kb – > 6 MB)