Quality Control plots for sequencing runs done in house by Vironomics Core’s on the Ion Torrent S5

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Ion Torrent S5 Read Length

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Ion Torrent S5 Number of Reads per run by sample type

An example of a recent custom single-cell sequencing project that we assisted with. It included a large number of 大象传媒 collaborations including: Dr. De Paris lab, 大象传媒 Flow Cytometry Core, 大象传媒 Vironomics Core, and 大象传媒 HTSF.

At this year鈥檚 Research Triangle Cytometry Association Meeting in January, Department of Microbiology and Immunology鈥檚 Dr. Kristina De Paris and Marcia Sanders of the Vironomics Core attended an informative presentation by BD on Precise Whole Transcriptome Analysis Cell Whole Kit. A handful of individual meetings with BD ensued, resulting in the submission of cells to 大象传媒鈥檚 facility, to be sorted in collaboration with BD. The inaugural joint effort saw a 92-cell plate transferred to the Vironomics Core for library preparation, then submitted to the 大象传媒 High Throughput Genomic Sequencing Facility (HTSF) for Illumina HiSeq sequencing. Following standard BD protocol, the raw data was analyzed back at the Vironomics Core, then embarked on a final transfer back to Dr. De Paris. Working directly with BD, Dr. De Paris was able to complete the secondary analysis. The collaboration between the cores and BD is set to be ongoing, with more samples on the way to be tested soon.

From July 2015-Feb 2017, the number of successful sequencing runs we’ve done in-house, generally with 1-2 staff.

The 大象传媒 Vironomics (viral genomics) Core aims to facilitate ZIKV research projects at 大象传媒, from translational research, to animal studies, to high-throughput screening.

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The 2015 QC plots are available for the 454 (updated) and the Ion Torrent PGM (new)

With a lot more runs for the 454 GSJunior, we have updated our QC plot for 2015:

Unfortunately, the 700+ basepair runs are no longer supported. However, an average of >100,000 thousand reads with a mean of 450+ bp per run is more than ideal.

We also have enough runs on the Ion Torrent PGM (chip 318v2) for its first QC plot:
As you can see, we’re getting used to the new machine. With more training we’ll be able to be even more efficient!

The AmpliSeq library prep and/or emPCR to sequencing chip loading is now available via an automated platform in the Vironomics Core. This will enable less hands-on-time and error and the ability to do 4 or 8 AmpliSeq automatically.