{"id":131,"date":"2010-10-15T15:10:52","date_gmt":"2010-10-15T19:10:52","guid":{"rendered":"http:\/\/www-test.bu.edu\/picf\/?page_id=131"},"modified":"2026-04-15T14:57:34","modified_gmt":"2026-04-15T18:57:34","slug":"genomics","status":"publish","type":"page","link":"https:\/\/www.bu.edu\/bif\/genomics\/","title":{"rendered":"Genomics"},"content":{"rendered":"

There are a few pieces of conventional PCR workflows in LSE452. Please discuss before using, as some of the equipment is available solely to support Xenium experiments.\u00a0 There is however, an Eppendorf Mastercycler Pro<\/a> that can be used for routine PCR. This machine will most likely be on the cloud scheduler due to increased demand. The MJ research cycler supports only v1 Xenium chemistry so it may be made available as people change to the V2 chemistry.<\/p>\n

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A quick note about quantitative real-time PCR.<\/p>\n

In recent years there has been a push to standardize nomenclature and methods to allow reproduction of experiments.<\/p>\n

From this desire, we get MIQE guidelines which is\u00a0M<\/span>inimum I<\/span>nformation for Publication of Q<\/span>uantitative Real-Time PCR E<\/span>xperiments.<\/p>\n

A growing number of journals are adopting these guidelines and it is worth considering when you are at the design phase.<\/p>\n

The initial publication may be found here<\/a> and a presentation (1hr) explaining it all here<\/a>.<\/p>\n

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qPCR<\/h2>\n

Our ABI 7900ht qPCR machine is configured with 384 well sample block. This cannot be changed by users so it is impossible to run 96 well plate.<\/p>\n

You don’t have to fill the 384 wells but the block requires that density plate<\/p>\n

The machine on the right side of the room is Real time #2<\/p>\n

Realtime #2 is currently the preferred machine for custom (longer than 2hr protocols).<\/p>\n

Please note the reservation blocks are 30 minutes to allow both reservations for analysis and<\/p>\n

custom runs (>2hrs)<\/p>\n

ABI 7900ht real time PCR machines user’s guide<\/a> and Primer express<\/a> 3.0 manual.<\/a><\/p>\n

RULES AND SOPS<\/h2>\n

This system is NOT on the network and data must be removed via USB drives<\/p>\n

Real Time #2 is a Windows 7 system where everyone simply logs into to SDS user account (no pwd)<\/p>\n

All data should be collected onto the D: drive, the User data folder specifically.<\/p>\n

You are responsible for removing your old data from the system.\u00a0 Failure to do so could\u00a0result in machine failure.<\/p>\n

DO NOT EVER turn off the 7900. it must remain on always<\/strong><\/p>\n

RT#2 uses SDS 2.4 for acquisition.\u00a0 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 2.4).<\/p>\n

I also have Primer Express 3.0 ( ABI primer design software)\u00a0 if anyone needs it.***Important note: Primer express will not run on a dual core machine (all new pcs) and neither software will run on Mac.\u00a0I have been able to get the software to run on Win7 64bit<\/p>\n

Be considerate of other users.\u00a0 Do not sign up for time slots you don’t need.<\/p>\n

Start on time.\u00a0 Runs take 2 hours and if you start your run late it will snowball throughout the day.<\/p>\n

IMPORTANT<\/strong>: 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.<\/p>\n

Do not write on your plates or set them on dirty counters.\u00a0 Any filth on the bottom of the plate gets baked on the block resulting in poor performance.<\/p>\n

Any concerns or problems, let Todd know<\/p>\n

\u00a0NOTE: The plate centrifuge has died in an irreparable manner.<\/h3>\n

It has been replaced with the Lab Hack Plate spinner. \u00a0More info here<\/a><\/p>\n

Agilent 2100 BioAnalyzer<\/h2>\n

On the first bench along the east wall, is the BioA. The Bioanalyzer is a chip based electrophoresis platform that allows analysis of RNA,DNA or protein (depending on the chip used).<\/p>\n

https:\/\/www.agilent.com\/en\/product\/automated-electrophoresis\/bioanalyzer-systems\/bioanalyzer-dna-kits-reagents\/bioanalyzer-dna-analysis-228248<\/p>\n

This is an excellent\u00a0BioA overview<\/a><\/p>\n

https:\/\/www.agilent.com\/en\/product\/automated-electrophoresis\/bioanalyzer-systems\/bioanalyzer-instrument\/2100-bioanalyzer-instrument-228250<\/p>\n

the most common use is to evaluate RIN score prior to sequencing RNA (.overview-rna-quality-automated-electrophoresis-5994-7327EN-agilent<\/a>)<\/p>\n

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NanoDrop One C-<\/h2>\n

We have a NanoDrop one with cuvette capability. There are currently no charges for use. It is imperative that users follow the posted rules for shutting the system down, cleaning the pedestal, and proper disposal of tips and waste.<\/p>\n

Turner 20\/20N –<\/strong><\/h2>\n

Tube-based luminometer with dispensers .<\/p>\n

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Imaging workflows in 632<\/h1>\n