March 2009

Dear Deep Sequencers,
   Since Nemo's "extreme makeover" in October, we have been running Paired-End analyses at least once a month and the turn around time for single reads has been greatly reduced. Illumina recently announced "long reads" (up to 75 bases from each end). We are in the queue for the adjustments and when this service is available we will send out a group email. The Paired-End primer sets as well as the Standard GDE sets are available through the core lab at cost. The Paired-End sequencing (PE) uses a different second PCR primer which incorporates a second sequencing priming site. Please specify WHICH primer set you used to build your library when you submit your samples (currently we have RNA, DNA and PE). If you would like a copy of the adapter, primer, and attachment sequences, please send us an email requesting "the primer PDF", this is available to researchers at UMassMed only.

DATA STORAGE !!!
R Drive space is now available http://inside.umassmed.edu/is/ENS/Rdrive.aspx

Discussion ListServe for Deep Sequencing User Group (DUG)
To join send email to nemo@list.umassmed.edu
To subscribe to announcements only
   email nemo@umassmed.edu with Subscribe-Nemo in the subject box

David Lapointe, PhD presentation from DUG meeting in March ( click here )

Analysis Tools for Deep Sequencing: Click Here

Some articles of Interest:
    NT Ingolia et al "Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling" ScienceExpress Feb 12, 2009 (RNA sequencers might find this interesting)  article
   RNA SEQ PAPER ! A Mortazavi et al "Mapping and Quantifying Mammalian Transcriptomes by RNA-SEQ" Nature Meth May, 2008 article
   DR Smith "Rapid Whole-Genome Mutational Profiling Using Next-Generation Sequencing Technologies" Genome Res  4 Sept, 2008 article
   There is article about BarCodes and indexing in the recent issue (Oct 08) of Nature Methods ( available online ). 
   PeakSeq - app for scoring ChIP-seq data - Nature Biotech 09 ( available online ).
   The January 2008 issue of Nature Methods (vol 5) has several useful articles about next generation sequencing (available online).

If you are preparing samples for submission, please fill out one of the Sample Tickets for each sample. Since samples may be run at different times, we need a tracking sheet for each one please.

We have posted the official Illumina versions of the protocols on the services page (see link in the left nav column). FAQs and Core Lab versions of these protocols are being posted as they become available. Additionally, we welcome any user-submitted information (please send it to Nemo at the email below).

Nice book ... explains the types of Deep Sequencing and the nature of the data "bottleneck". Next-Generation Genome Sequencing: Towards Personalized Medicine, Edited by Michal Janitz. Wiley-Blackwell 2008.

To join the email list or send us a note use   nemo@umassmed.edu 

Thank you,

~ Nemo and Crew 

For a letter of support for a research grant click here.