Global analyses platform - Illumina Deep Sequencing

Illumina Genetic Analysis Platform - Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany

The HZI Illumina infrastructure is part of the Department of Genome Analysis of the HZI, one of the 16 large research organisations of Germany. The facility includes several robotic systems, large scale genome sequencing instruments (two Megabases, one HITACHI, four long range sequencers) including the most recent addition of an Illumina Genetic Analysis Platform. Highlights for digital gene expression tag profiling using Illumina analyser are:

  • No sequence knowledge required: Universal platform to study any transcript

  • Tuneable coverage: Almost unlimited dynamic range for rare transcript discovery

  • Sensitivity: Four million tags per sample yields an average of 12 counts for transcripts at one copy per cell

  • Orthogonal validation: Genome-wide data comparable to qPCR validation of microarrays.

The members of the infrastructure have more than a decade of experience in high-throughput genome sequence analysis. This involves large-scale DNA sequencing, bioinformatics and robotics including technology development. The department has been involved in a number of international and national genome projects.

As partner in TRANSVAC, HZI offers deep sequencing and comparative transcriptome analysis service based on the Illumina platform in the form of samples (RNA/DNA) analyses to be provided by external Users. The Users shall also be trained on site.

On-site access

Training for two Users at a time

  • theoretical and practical sample preparation (duration two days)
  • demonstration of sequencing process
  • theoretical and practical training of data processing (duration two days)

Modalities of access

Organisation short name: HZI

Unit of access: One sample (a sample of RNA, in a few cases DNA) to be analysed by Illumina Platform for sequencing and or transcriptome mapping on contract.

Quantity of access available: 160 samples (five Users)

Timelines: Approximately 10 weeks

Overview of access provided between January 2011 (1st call) and April 2013 (10th call):
Min. quantity of access to be provided: 160
Estimated number of users/User groups: 5
Estimated number of projects: 10
Access already provided: 146
Access still available: 14

Last call submission date scheduled for: This service is only available via paid access. The application period for the call is now closed.

Input – sample requirements:

RNA (or DNA) samples to be provided by Users. Samples to be processed should be 1–10 μg of total RNA. Check total RNA integrity following isolation preferably using an Agilent Technologies 2100 Bioanalyzer with an RNA Integrity Number (RIN) value greater than 8. High quality RNA will show a 28S rRNA band at 4.5 kb that should be twice the intensity of the 18S rRNA band at 1.9 kb. Both kb determinations are relative to a RNA 6000 ladder. The mRNA will appear as a smear from 0.5–12 kb. For other arrangements please contact the platform directly.

The DNA samples to be processed should be 1–5 μg of highly purified DNA in a total volume of 50 μl of TE buffer, having an OD260/280 ratio of between 1.8 and 2, and should be as intact as possible.

Output – deliverables to User:

The sequence raw data output will be stored in electronic format and delivered to the Users in FASTQ and FASTA formats. Analysed data will be delivered in comma separated text files (*.csv) or Microsoft Excel sheets (*.xls).

Contact

Michael Jarek

michael [dot] jarek [at] helmholtz-hzi [dot] de

+49 531 6181 5318