Service

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 II (GA II) sequencers and one Roche 454 FLX sequencing instrument.

Sequencing service is offered to the CRG, PRBB, and external users. We perform ChIP-Seq, RIP-Seq, digital gene expression profiling, mRNA sequencing, miRNA discovery and expression analysis, amplicon sequencing, re-sequencing, and de novo sequencing.

Starting from DNA or RNA samples provided by the users, we prepare sequencing libraries (including attachment of platform-specific adapters) and run the Illumina GA II or 454-FLX sequencing instruments. The resulting raw image data are converted into sequence data (sequence files, quality files, alignment files) which are made available to the users by ftp file transfer.

Service fees

Please contact Heinz Himmelbauer for requests.

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 the Unit leader (heinz.himmelbauer@crgNOSPAM.es), 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 ( doc, pdf). 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 !

Sequencing Platforms

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.

Illumina Sequencing Sequencing workflow Sample preparation Data processing and analysis
454 Sequencing Sequencing workflow Sample requirements Data processing Post sequencing software applications Useful SFF Tool commands Multiplexing samples