November 2009

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

Paired-End Sequencing
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 SR 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.

Expanded Options
The upgrade for longer reads is available. Your run choices are Single-Read 36 or 76 bases and Paired-End 36+36 or 76+76. We need at least 7 of a particular format to run the instrument. If you have SR76 or PE76+76 coming up please let us know so we can put the word out and gather up enough folks for a whole run.

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

A Few Words About "The Number of Reads" or "Cluster Count" on the Illumina Platform
There are several reasons why your library may not be generating the large number of reads you are expecting:
1. "Stuff" in the sample is contributing to the quantification but does not have the capacity to form clusters (e.g. stray primers)
2. The library was built using custom adapters, and only one end of the fragment now has the sequence priming site, but both ends have attachment sequences (you will only get sequencing from half of the clusters seeded, ie lower counts by 1/2)
3. The library was built with PCR1.1 and PCR2.1 primers which do not have the modifications
4. Quantification of the library is not accurate
5. Sizing of the library is not accurate or as tight as it should be

For Information about the new SOLiD Analyzer click here

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.