View source for Help:2013 DNA Distribution

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The DNA Distribution has been entirely revamped this year! Whether you’re new to iGEM and the Registry of Standard Biological Parts or an experienced participant, please make sure to read through the Distribution Handbook.
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The 2013 Distribution contains over 1000 part samples as dried (miniprepped) DNA, with each sample [[Help:Quality_Control|QC tested]] through [[Help:Quality_Control#Sequencing_Results|sequencing]], [[Help:Quality_Control#Antibiotic_Test_Plates|AB test plates]], and [[Help:Quality_Control#Gel_Results|restriction digests]]. While there is not enough DNA for assembly, you will be able to [[Help:Distribution_Kits#DNA Kit Plate Instruction|transform the DNA]] into cells and then make your own glycerol stocks of any part you wish.

==What's included in the 2013 Distribution==
[[Image:2013_distribution.jpeg|690px|center]]

Your Spring 2013 Distribution contains the following:
* DNA Distribution Kit Plates 1 - 4
* DNA Distribution Kit Plate 5 (Supplemental Plate)
* Linearized Plasmid Backbones: pSB1A3, pSB1C3, pSB1K3.m1, pSB1T3
* [https://parts.igem.org/Help:Transformation_Efficiency_Kit Transformation Efficiency Kit]
* iGEM Stickers and Pins! (iGEM teams only)

If there is an issue with your distribution kit, please send us an email to ''hq (at) igem . org''

==Getting Started==
If you're new to the Registry, iGEM, or synthetic biology, you'll want to read through our Help pages before you get started. The [[Help:Learn|Learn section]] is the best place to start, and will take you through the basics.

Otherwise, <b>read on!</b>

===Locating a Part in the Distribution===
Before using the DNA plates, you should [[Help:Locating_Parts|search the Registry]] for useful parts, which will also tell you if it has an available sample, its location (if they're in your 2013 Distribution), requirements, quality control (if they're correct), etc.

====Searching====
*The '''[[Help:Locating_Parts|Catalog of Parts and Devices]]''' will allow you to browse parts and devices by various criteria, including function, chassis, standard, etc.
*The '''[[Help:Locating_Parts|Search Tools]]''' will let you search by text or part name <more>.
*It is also possible to see the contents of the Kit Plates in their entirety. You can look at the [https://parts.igem.org/cgi/assembly/libraries.cgi DNA Repositories] section on the main page.
**Click on [https://parts.igem.org/assembly/libraries.cgi?id=51 2013 Distribution] to see the contents of all of your kit plates. 
**Click on the 2013 Kit Plate of your choice, which will list all parts by their part name (BBa_..) in a plate along with their quality control information. Or you can click on the small part diagram below each Kit Plate link: "See a summary of the parts in this plate." 
**These options will show you what is in each well of your plate, however they are not the best way to find specific parts you would like to use.

====Part Main Page====
When you find a part you can learn all about it by going through its [[Help:Nav/Part_Main_Page|main page]] and sub-pages.

===Availability===
If you find a part that you would like to use, you need to make sure that a sample of the part is actually available. There are many parts in the Registry that people are still working on, or decided not to continue working on anymore, therefore we never received or do not yet have the physical DNA for them.  This of course means that the DNA is not available in the Spring 2013 DNA Distribution.  The simplest way to tell whether the part has an available sample is to look at the top right of the part's Main Page.  If the part has an available sample the top part of the box will be green and say "DNA available."

===Requesting a part===
We've taken care to create a very well-rounded DNA Distribution this spring, however, should you find the part, or parts, that you require are not available in the distribution but available in the Registry's Repository, send us an email (hq [AT] igem [DOT] org) in order to request a sample. Just include the part name, the plasmid it's located in, and the source, and we'll send it out to you. For more information please see the [[Help:Requesting_Parts|Requesting Parts page]]

===Using the online QC resources===
Here at Registry, we want everyone to take a look at the results of the [[Help:Quality_Control|quality control measures]] we've taken this year and previous years, in order to make an informed decision when choosing to use a part. We've made sure to update the online repository for the Spring 2013 distribution with our quality control results.

The best way to use our quality control information is to use it on a part by part basis. As you design your project, make sure to check every part that you're interested in for its QC data. After searching for a part in the registry and arriving at its main page, click on the '''Get This Part''' link which will take you to the section listing various quality control information for a samples of that part and its location within the registry.


==Using the Spring 2013 DNA Distribution==
===Storage===
Since the distribution kit plates are comprised of dried DNA, they are quite stable for storage at room temperature. However once the DNA is resuspended in any of the wells, we recommend either storing the kit plate with its plastic cover in a -20C freezer, or aspirating the rest of the resuspended DNA from the well and keeping it separately in a -20C freezer.

The linearized plasmid backbones (25ng/ul at 50ul) should be stored at 4C or lower.

===DNA Kit Plate Orientation===
<html>
<iframe src="http://player.vimeo.com/video/25202556" width="500" height="281" frameborder="0" webkitAllowFullScreen mozallowfullscreen allowFullScreen></iframe> <p><a href="https://igem.org/Videos/Locating_Your_Part">Locating Your Part</a> from <a href="https://igem.org/Videos">iGEM Videos</a>.</p></html>

[[Image:IGEM06DistPlateTop.jpg|right|thumb|200px|Top view of plates containing dry DNA; <font color="red">red</font> circle indicates well 13H]]

The foil covers on each 384 well kit plate can be easily punched through with a pipette tip into the well of your choice. Unfortunately, the foil cover will also obscure both column and well markings. You can still find your part by correctly orienting the plate using the two notched corners as markers: well '''A1''' is located at the upper left corner of the plate when the long side of the plate with the notched corners is considered the bottom.

Once you know the location of your part, you will 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 oriented at the BOTTOM of the plate (see the "top view" image on the right for correct orientation)''

===DNA Kit Plate Instructions===
To use the DNA in the Distribution Kit you may follow these instructions:
:# With a pipette tip, punch a hole through the foil cover into the corresponding well of the Biobrick&trade;-standard part that you want. [https://parts.igem.org/Help:Spring_2011_DNA_distribution#DNA_Kit_Plate_Orientation Make sure you have properly oriented the plate]. We recommend that you do not remove the foil cover, as it could lead to cross contamination between the wells.
:# Pipette 10uL of dH2O (distilled water) into the well. Pipette up and down a few times and let sit for 5 minutes to make sure the dried DNA is fully resuspended. We recommend that you do not use TE to resuspend the dried DNA.
:# [[Help:Transformation_Protocol|Transform]] 1 or 2uL of the resuspended DNA into your desired competent cells, plate your transformation with the appropriate antibiotic* and grow overnight.
:#Pick a single colony and inoculate broth (again, with the correct antibiotic) and grow for 16 hours.
:#Use the resulting culture to [http://openwetware.org/wiki/Miniprep/Kit-free_high-throughput_protocol 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]). We recommend using the miniprepped DNA to run QC tests, such as restriction digests and sequencing.

''* 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.''

''Note: There is not enough DNA in each well to perform anything but [[Help:Transformation_Protocol|transformations]]''

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===Linearized Plasmid Backbones===
The 2013 Distribution Kit also includes a set of four linearized plasmid backbones: pSB1A3, pSB1C3, pSB1T3, and pSB1K3.m1. These plasmid backbones have been prepared via PCR and purified. Prior to ligation the linearized backbones will need to be digested with with EcoRI, PstI and DpnI (DpnI is optional: to cut up original template DNA used to create linearized plasmid backbone), leaving two ends ready to be ligated to a Biobrick&trade; part. All 2013 submissions will need to be in pSB1C3, so we recommend using our pSB1C3 linearized backbone for that purpose. 

You can find more in depth instructions on how to use and make your own linearized plasmid backbones on the [[Help:Protocols/Linearized Plasmid Backbones | protocol page]]. ''Note: The linearized plasmid backbones need to be cut by EcoRI and PstI restriction enzymes prior to use.''


[[Help:Production/2012 Plasmid Backbones| 2013 Plasmid Backbone Production]]
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===Transformation Efficiency Kit===

We have included a [https://parts.igem.org/Help:Transformation_Efficiency_Kit transformation efficiency kit] in the 2013 distribution to help you troubleshoot cloning trouble. The single biggest reason your transformations don't work usually comes down to the efficiency of your competent cells. If you use this protocol, you can test the competency of your cells and more easily find problems. 


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