Submit a Sample

In order to help the BSF staff ensure smooth operation and high-quality service, all users are asked to adhere to the following sequencing workflow as much as possible. In particular, a carefully completed sample annotation sheet and sequencing authorization form should be submitted prior to (or together with) the sample submission. If these forms are not available or contain insufficient information, the submitted samples may lose their scheduled slot in the sequencing queue be rescheduled only once all required information has been submitted!

Step 1: Planning

  • For new projects, it is recommended to arrange a meeting with members of the BSF team to discuss study design and obtain recommendations for sample preparation. This is particularly important for larger projects (>50 samples) that require significant BSF resources to be completed in a timely manner. In contrast, for very small projects (less than 4-8 samples), it is usually advisable that scientists collaborate with a research group that already sends samples to the BSF, in order to minimize risk of failure and logistical overheads (which tend to be increased for first-time users).
  • In particular, to be eligible for subsidized prices under the "Collaborative Sequencing" framework, users have to provide evidence that suitable arrangements have been made for the analysis and interpretation of the sequencing data, as outlined in the section on Bioinformatic Analysis.
  • Sequencing library preparation can be performed either by the user (recommended for regular users and those with special demands) or by BSF staff, depending on the protocol.
  • BSF staff schedules samples for sequencing in a fair and transparent manner. When samples are submitted in batches that fill a flowcells (8 libraries), it is relatively straightforward to estimate sequencing completion dates (typically in 2-4 weeks). Alternatively, users can submit samples in arbitrary batches, in which case the time to completion depends on users to fill up the flowcell run and is sometimes hard to predict (but rarely longer than 6 weeks). Early notice about upcoming samples and priorities facilitates scheduling and tends to decrease turn-around time. On top of the time to sequencing completion comes the bioinformatic processing time, which depends heavily on the amount of bioinformatic support requested.

Step 2: Preparation

  • All users who want to take advantage of the BSF data processing service or submit their samples in batches of less than eight libraries (equivalent to one flowcell) must submit a comprehensive sample annotation sheet.
  • The sample annotation sheet can be downloaded from the Download page, and the filled-in version should be e-mailed to the This email address is being protected from spambots. You need JavaScript enabled to view it. for review a few days prior to sample submission to avoid delays.
  • Once library preparation has been completed, carefully labeled tubes containing the libraries are handed over to the This email address is being protected from spambots. You need JavaScript enabled to view it. (in person or via mail). The labels must be exactly identical with the "library name" in the submission sheet.
  • In addition, to comply with various regulations the principal investigator needs to fill out the sequencing authorization form and e-mail a signed PDF copy to the This email address is being protected from spambots. You need JavaScript enabled to view it..

Step 3: Sequencing

  • Upon receipt of all three items - sample annotation sheet, tubes containing the submitted DNA libraries and sequencing authorization form - the libraries will be scheduled for quality control.
  • Quality control is performed by BSF staff to assess whether the libraries are of sufficient quality (Bioanalyzer/Experion) and quantity (Qubit) for sequencing. If not, the user is informed and asked to submit new libraries.
  • Libraries that have passed quality control are scheduled for sequencing, which involves three main steps: cluster amplification on cBot, sequencing on HiSeq 2000 and data processing.
  • Sequencing data are typically returned in the format of unaligned BAM files. In addition, for common protocols a detailed analysis report is generated and made available to the user.

 Step 4: Follow-up

  • Billing and payments are being administered by the finance department of CeMM (administrative contact: This email address is being protected from spambots. You need JavaScript enabled to view it.) or by the core facilities of the Medical University of Vienna.
  • All analysis reports are stored for at least six months. Extension of the storage time is possible on request. Data for samples without sample annotation sheet will be deleted after two month unless it has been discussed otherwise. 
  • For sequencing performed under the framework of “collaborative sequencing” or “joint protocol development”, the user is required to inform the BSF coordinator prior to submission of any publications arising from collaborative sequencing and to acknowledge the BSF through co-authorship and/or a suitable sentence in the Acknowledgement section (jointly decided based on the scope and scale of the BSF contribution).
  • The BSF provides free support for certain tasks required for finalizing manuscripts, e.g. providing paragraphs for Methods section and depositing sequencing data into public repositories.