The sequencing field has experienced a major shift with the introduction of innovative, high-throughput sequencing technologies developed by Solexa/Illumina and 454/Roche. The Ultrasequencing Unit at the CRG
is presently equipped with two Illumina Genome Analyzer IIx
(GA IIx) sequencers, one Illumina HiSeq2000
sequencer and one Roche 454 FLX
Sequencing service is offered to the CRG, PRBB, and external users. We perform ChIP-Seq, mRNA-Seq, sequencing of small RNA molecules such as miRNA, amplicon sequencing, genome re-sequencing, and de novo sequencing.
Starting from DNA or RNA samples provided to us, the service includes:
1. Sequencing library preparation incl. attachment of platform-specific adapters
2. Library quality control
3. Library quantification
4. Performing the sequencing run
5. Basecalling data, sequence data quality control, making data available (sequence files, quality files, alignment files)
Please contact Heinz Himmelbauer
Rules for ordering sequencing services and for communication with the staff of the Ultrasequencing Unit
1. Before bringing samples to the Unit, please discuss the project with the Unit leader. We prefer that you send an e-mail with an outline of your project to Heinz Himmelbauer
, so that we can discuss the experiments in detail and find the best strategy for dealing with your project.
2. Based on the agreed procedure, we will issue a quotation for the service.
3. Following your approval of the service quotation (please indicate which account can be charged for the work), please submit your samples to the Unit’s staff, along with the filled in request form
. In order to reduce interference with the Unit’s workflows, hand your samples over to lab staff only Monday, Wednesday, or Friday from 11 am to 1 pm. Avoid interrupting anyone who is busy. If they were working with your samples, you would not like to have them disturbed !
4. Once your samples have arrived in the Unit, we can start planning with them (sample preparation; quality check; assigning the samples to sequencing runs).
5. If you have specific technical questions or concerns about your samples, e-mail us.
6. We are happy to assist in the analysis of the data. Please e-mail us ahead of time to schedule an appointment.
7. Once you have analyzed your data, any feedback is welcome. The Unit depends on your input to improve the services that we offer !
The Illumina and 454 platforms complement each other very well. While Illumina sequencing generates millions of short reads per run (presently 36-50 nt reads), 454 reads (Titanium chemistry) exceed 400 nt, though data sets are smaller. Thus, Solexa is the ideal platform for projects that require large numbers of short reads e.g. ChIP-Seq and miRNA detection experiments, while 454 is more suitable for projects that benefit from the information that longer reads provide, e.g. de novo sequencing and transcriptome characterization in the absence of a reference genome.