From OpenWetWare


  • Improvements in Microarray Processing
  • Improvements in Illumina Sequencing
  • Pilot project for large scale data storage
  • BioMicro Center renovation ongoing.

It has been a few months since our last update and I would like to share with everyone several improvements we have made in some of our core technologies.

One large change has been in our handling of microarrays. Affymetrix will be retiring their old labeling kits later this year and we have been evaluating different technologies to replace the old kits. We have tried out new kits for both eukaryotes and prokaryotes and have been pleased with the results. Both new kits require significantly less sample input (<100 ng total RNA) and are easier to handle larger numbers of samples. We are also looking at other labeling techniques that would require even less input RNA (<1ng or even from single cells). More information can be found on our website. If you are interested in some of the newer technologies, please contact Manlin or myself.

In addition to microarrays, we have also upgraded to the latest kits from Illumina for next-generation sequencing. These new kits replace the old cleavage buffer with a new formulation that allows for much longer reads. We have preformed some tests with these new kits and have been able to achieve read lengths of 144nt (72nt each from the front and back) with over 90% of the reads showing 1 error or less at densities of typically >5 million reads per lane. We have placed some of the preliminary analyses on our website under the genomic sequencing section.

We have also started a pilot program to help labs handle the large amounts of data produced by these high-throughput methodologies in response to requests from several labs. We have purchased a new storage server and are providing space on the server at $500 per terabyte per year. The server is set up to be able to be accessed from all three major operating systems (Linux, Windows and Mac) and the data is backed up using MIT’s TSM (normally $65/mo). Space on this pilot server is limited and will be allocated on a first come / first served basis. Please contact Stephen Goldman or myself if you have questions. More information about this program can be found in the computing section of our website.

Lastly, we are still in the process of remodeling the BioMicro Center lab space. Thank you all for your patience as we have been in transition and we hope by the end of this month to have the process completed. The final layout is also on our website along with all of our monthly updates.