Genomics

A quick note about quantitative real-time PCR.

In recent years there has been a push to standardize nomenclature and methods to allow better reproducibility and fidelity in studies.

From this desire we get MIQE guidelines which is Minimum Information for Publication of Quantitative Real-Time PCR Experiments.  A growing number of journals are adopting these guidelines.

The initial publication may be found here and a presentation (1hr) explaining it all here.

 

The cornerstone of our genomics component are two real time PCR machines.

These ABI 7900ht qPCR machines are both configured with 384 well sample block.

The machine on the left side of the room is Real time #1

The schedule for this machine can be found by click the name above.

The machine on the right side of the room is Real time #2

Realtime #2 is currently the preferred machine for custom (longer than 2hr protocols).

Please note the reservation blocks are 30 minutes to allow both reservations for analysis and

custom runs (>2hrs)

ABI 7900ht real time PCR machines usersguide and Primer express 3.0 manual.

RULES AND SOPS

These systems are NOT on the network and data must be removed via USB drives or cd’s

They are Windows 2000 systems and require that you log in to your lab’s account (set up by the core administrator).

All data should be collected onto the D: drive the User data folder specifically.

You are responsible for removing your old data from the system.  Failure to do so will result in machine failure.

Log off when you are done using the system.

Realtime 1 uses SDS 2.3, RT#2 uses SDS 2.2.2 for acquisition.  There is a version of the software for off-line analysis that you can install on lab PC’s for data analysis and plate layout (SDS 2.3).

I also have Primer Express 3.0 ( ABI primer design software)  if anyone needs it.

***Important note: Primer express will not run on a dual core machine (most new pcs) and neither software will run on Mac.

I have been able to get the software to run on Win7 64bit

Be considerate of other users.  Do not sign up for time slots you don’t need.

Start on time.  Runs take 2hours and if you start your run late it will snowball throughout the day.

If you plate is running into someone’s time slot, They have the right to abort the run a dispose of your plate! So if you are running late check the schedule before starting, and notify any effected parties.

Do not write on your plates or set them on dirty counters.  Any filth on the bottom of the plate gets baked on the block resulting in poor performance.

Any concerns or problems, Please notify me right away.

 

Axon GenePix 4000b is available  in LSEB 448. (Calendar)

 

***This system is controlled by a Windows NT system and is a bit finicky.  It is on the network but does not support USB.  It requires initial training and approval for use.  Once a user is rated for unassisted use, the machine may be accessed via card swipe through 452.

***(09/22/11)Super awesome good news- The Genepix system has been upgraded. It is now Windows 2000 and supports USB!!!

It also has a drastically larger hard-disk and New version of Genepix!

Some useful files are available for download like the Axon GenePix4000B manual and app notes PMT adj and  Signal to noise

 

Genomics Billing

The ABI systems are under contract and users split the cost proportionally.

The GenePix system has no contract and users split the costs of repairs.