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Genome Center

 
Head
Detlef Weigel, Christa Lanz
Secretary:
Hülya Wicher
Phone:
+49 7071 601-1411
Fax:
+49 7071 601-1412

Introduction

Managed by Detlef Weigel and Christa Lanz with assistance from Andrea Belkacemi, the genome center is equipped with both Sanger and next generation sequencing facilities.

With the ABI3730xl 96-well capil­lary sequencer (installed in 2002) the genome center offers small-scale service sequencing, for example to verify plasmid constructs and high-throughput sequencing or to shot gun sequence BACs and fosmids. Annual throughput has increased from 72,000 samples in 2003 to over 119,000 samples in 2014. The average read length on the 3730xl is 700 to 800 bases for standard DNA samples with a maximum read length of 1,100 bp. The output per day is about 1 Mb of total sequence. Importantly, turn around time, from receiving the samples to return­ing the sequences, is less than 12 hours on average.

The institute was one of the first on the continent to install Illumina (formerly Solexa) short read sequencers in 2007. Instruments have been constantly upgraded, and the facility currently operates a MiSeq instrument, acquired in 2012, and a HiSeq3000 instrument, acquired in March 2015. Throughput has increased dramatically, from around 1 Gb per run (first GA instrument) to over 90 Gb (GAIIx), 350 Gb (HiSeq2000) and 800 Gb (HiSeq3000.) This increase was due both to moving from shorter single end reads to longer paired end reads, and also to various hardware improvements. With the HiSeq3000 instrument, the genome center provides high-throughput sequencing at an attractive per-base-costs and a short turn around time.

Equipment

Sequel (PacBio)
Hiseq3000 mit cBot (Illumina)
Miseq (Illumina)
ABI 3730xl DNA Analyzer (Applied Biosystems)
Pipetting robot (Beckman Coulter Biomek® 2000)
DNA isolation robot (Qiagen BioRobot 8000)
S2 Series (Covaris)
Hydroshear plus
Megaruptor v2 (Diagenode)
Qubit (Invitrogen)
CHEF-DR III (Bio-Rad)
BluePippin (Sage Science)
Sage ELF (Sage Science)
ALFS 50V (Thermo Scientific)
2100 Bioanalyzer (Agilent Technologies)

Applications

Genome sequencing of different species, such as bacteria, plants and nematodes. 
Mapping and mutant identification by sequencing. 
Sequencing of chromatin immunoprecipitated material (ChIP-seq). 
Small RNA and transcriptome analyses (sRNA-seq and RNA-seq).