Difference between revisions of "Help:IGEM 09 DNA distribution"
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Workflow,
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==Storage==
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Store the DNA Parts Kit with the plastic lid and the adhesive foil cover in the -20C freezer.
  
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3/26/09
 
  
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PlateMatePlus Training and Test Runs
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==Usage==
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The DNA Parts Kit is a tool available to you to perform synthetic biology with standard biological parts. It contains dry DNA of ALL of the parts that are available in the Registry up until May 2007. You will transform the DNA into cells and make your own glycerol stocks of any part that you wish. It does not contain enough DNA to do assembly.  To use the DNA in the Parts Kit follow the following instructions:
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:# Puncture a hole through the foil with a pipette tip into the well that corresponds to the Biobrick™-standard part that you want
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:# Add 15 uL of diH2O (deionized water)
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:# Take 1uL DNA and [http://openwetware.org/wiki/Bacterial_Transformation transform] into your desired competent cells, plate out on a plate with the correct antibiotic'''*''' and grow overnight.  Your goal here is to obtain single colonies. 
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:#Pick a single colony and inoculate broth (again, with the correct antibiotic) and grow ~18 hours.
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:#Use the resulting culture to miniprep the DNA AND make your own glycerol stock (for further instruction on making a glycerol see [http://openwetware.org/wiki/Endy:Making_a_long_term_stock_of_bacteria this page]).
  
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<small>'''*'''To know which antibiotics to use, look at the plasmid that the part is in.  The [https://parts.igem.org/wiki/index.php/Help:Plasmids/Nomenclature naming scheme] for plasmids is specifically designed to indicate antibiotic resistance.</small>
  
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- picture of PMP goes here
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==Part location in distribution plates==
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[[Image:IGEM06DistPlateTop.jpg|left|thumb|200px|Top view of plates containing dry DNA; <font color="red">red</font> circle indicates well 13H]]
  
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CLEANING PROCEDURES:
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All of the DNA Parts Kit plates are Nunc 384-well plates. Unfortunately, the foil cover goes over the column and well markings.  However, you can still correctly orient the plate using the two notched corners: well '''A1''' is in the upper left corner of the plate when the long side of the plate with the notched corners is considered the bottom.
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When cleaning the tips we used H20, however we can use a pre-made solution as well. However, if we have enough cassettes, than we may not need to run cleaning cycles during use.
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We were trained by Tsultrim on the use of the PMP.
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Once you have found out which well your BioBrick&trade; part of choice is in by searching for it in the Registry (for example well 13H in iGEM2007 DNA Parts Kit Plate 1) you want to count across the plate starting with Column 1 until you get to Column 13 and down the plate starting with Row A until you get to Row H.
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Located existing program by Mac, which seems to work well. We will likely use this program with some modifications. The basic elements of the program will be detailed later.
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The current program, takes into consideration a margin of 50ul that the machine will be unable to aspirate, this is because (a) the pipette tips do not reach to the bottom of the well when aspirating from the 384 Deepwell plates, and (b) a few ul s will be lost.
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If we start with a source plate with 200 ul in each well, than that margin would leave 150 ul to be dispensed into 50 plates at 3 ul per well each.
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We'll discuss further the merits of using 5ul, rather than 3 ul, if needed.
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Possible improvement: starting off the aspiration shallower from the well, and then move deeper.
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'''MAKE SURE that the two notched corners of the plate are the BOTTOM  two corners (see the top view image at left for correct orientation)'''
  
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384 replication workflow:
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<br style="clear:both;"/>
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Roughly 800 to 1000 parts
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Delivered as (3) 384 well plates x (200) kits total, will mean a production of 600 total
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200 ul into each well of the source plate,  - 50ul margin, divided by 3ul into each well, will give us 50 plates per original source plate
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4 copies of single source plate will give us the needed amount to make all of the kits (200), x (3) source plate types, will be 600 total sent out.
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We need to discuss details of the EP5075 robot further
 
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Notes:
 
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- need to order new cassettes for 384w/30ul pipettes
 
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- best time to work is after 3pm
 
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Updated on 3/26/09
 
  
 
==Locating a Part in the Distribution==
 
==Locating a Part in the Distribution==

Revision as of 15:57, 27 March 2009

iGem 2009 Distribution

This year the parts will sent out in (3) 384 well plates, while we will not sending out all of the parts in the Registry, we have taken extra measures and done extensive selection to create a kit with a small number of high quality parts. The 384 well plates hold dry DNA, and will be a starting point for your projects.

To use the DNA in the Parts Kit follow the following instructions:


Storage

Store the DNA Parts Kit with the plastic lid and the adhesive foil cover in the -20C freezer.


Usage

The DNA Parts Kit is a tool available to you to perform synthetic biology with standard biological parts. It contains dry DNA of ALL of the parts that are available in the Registry up until May 2007. You will transform the DNA into cells and make your own glycerol stocks of any part that you wish. It does not contain enough DNA to do assembly. To use the DNA in the Parts Kit follow the following instructions:

  1. Puncture a hole through the foil with a pipette tip into the well that corresponds to the Biobrick™-standard part that you want
  2. Add 15 uL of diH2O (deionized water)
  3. Take 1uL DNA and [http://openwetware.org/wiki/Bacterial_Transformation transform] into your desired competent cells, plate out on a plate with the correct antibiotic* and grow overnight. Your goal here is to obtain single colonies.
  4. Pick a single colony and inoculate broth (again, with the correct antibiotic) and grow ~18 hours.
  5. Use the resulting culture to miniprep the DNA AND make your own glycerol stock (for further instruction on making a glycerol see [http://openwetware.org/wiki/Endy:Making_a_long_term_stock_of_bacteria this page]).

*To know which antibiotics to use, look at the plasmid that the part is in. The naming scheme for plasmids is specifically designed to indicate antibiotic resistance.

Part location in distribution plates

Top view of plates containing dry DNA; red circle indicates well 13H

All of the DNA Parts Kit plates are Nunc 384-well plates. Unfortunately, the foil cover goes over the column and well markings. However, you can still correctly orient the plate using the two notched corners: well A1 is in the upper left corner of the plate when the long side of the plate with the notched corners is considered the bottom.

Once you have found out which well your BioBrick™ part of choice is in by searching for it in the Registry (for example well 13H in iGEM2007 DNA Parts Kit Plate 1) you want to count across the plate starting with Column 1 until you get to Column 13 and down the plate starting with Row A until you get to Row H.

MAKE SURE that the two notched corners of the plate are the BOTTOM two corners (see the top view image at left for correct orientation)



Locating a Part in the Distribution

Browsing through the "plates"

  1. Go to the Registry.
  2. Click on DNA Repositories in the toolbox.
  3. Click on Spring 2009 Source Plates.
  4. Here you will find a list of all 22 96-well "plates" that comprise the 2009 Spring DNA Distribution. You can browse through all of the plates and take a look at all of the Quality Control information.

Locating a particular part

  1. Go to the Registry.
  2. In the search box on the upper left, enter the part number that you are interested in (e.g. BBa_B0015) and click GO.
  3. In the part navigation bar at the top of the page, click on Physical DNA.
  4. You will see all of the locations for this part. You are looking for the location in the Spring 2008 Distribution Library
    • Note that we only have physical DNA for parts whose part status (box in the upper right hand corner) reads Available