Difference between revisions of "User:Meaganl/Online DNA Submission Instructions"
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When you come to the DNA Submission main page, you will be able to “start a new DNA submission” or “see your DNA submissions.”  To begin the submission process click on “start a new DNA submission.”
 
When you come to the DNA Submission main page, you will be able to “start a new DNA submission” or “see your DNA submissions.”  To begin the submission process click on “start a new DNA submission.”
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[[Image:DNA_Submissions__main_page_options.tiff|400px|center]]
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[[Image:Contact_info_check.tiff|500px|left]] On this page that you must enter information about yourself as the user submitting the DNA.  Please make sure that the username and full name that we have listed for you is correct.  You then need to choose which team you are on (also called a group).  Correct your email if necessary and do not forget to enter your phone number. 
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You must tell us in what format you are sending your DNA.  Choose a format from the drop-down menu and indicate how many samples you are sending.    Click [[DNA Submission Formats|'''here''']] for more information about the accepted formats.  You should also let us know if there are any special instructions that we must know about.  <font color=red>[IMAGE]</font>
  
  
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On this page that you must enter information about yourself as the user submitting the DNA.  Please make sure that the username and full name that we have listed for you is correct.  You then need to choose which team you are on (also called a group).  Correct your email if necessary and do not forget to enter your phone number. 
 
  
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You must tell us in what format you are sending your DNA.  Choose a format from the drop-down menu and indicate how many samples you are sending.    Click [[DNA Submission Formats|here]] for more information about the accepted formats.  You should also let us know if there are any special instructions that we must know about. 
 
  
 
Keep in mind that there are specific DNA amount requirements that you must follow.  
 
Keep in mind that there are specific DNA amount requirements that you must follow.  
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Now you may proceed to entering sample information by clicking on the button at the bottom of the page. At the top of the sample information page you will see your Shipment #.  You will need to remember this number, in particular if you are sending your DNA in filter paper grid format.  In this case the shipment # needs to be written clearly on the filter paper grid form.   
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Proceed to entering sample information by clicking on the button at the bottom of the page. [[Image:Proceed_to_sample_info.tiff|350px]]
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At the top of the sample information page you will see your Shipment #.  You will need to remember this number, in particular if you are sending your DNA in filter paper grid format.  In this case the shipment # needs to be written clearly on the filter paper grid form.   
  
 
Begin to enter the information for your first part, beginning with the part number.  You must enter the plasmid that the part is in.  Note that the software will only recognize plasmids that are documented in the Registry so if you haven’t added your plasmid to the Registry you must do so before submitting your parts.  See the “Notes” section below for more details on plasmid information.   
 
Begin to enter the information for your first part, beginning with the part number.  You must enter the plasmid that the part is in.  Note that the software will only recognize plasmids that are documented in the Registry so if you haven’t added your plasmid to the Registry you must do so before submitting your parts.  See the “Notes” section below for more details on plasmid information.   
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Once you have entered the part number and plasmid for your part, you can tab over to the antibiotic resistance field.  The software will automatically fill in the antibiotic resistance based on the plasmid that you have entered.  Please check to make sure that the resistance is correct.  You may change it manually if it is not correct.  The antibiotic abbreviation is the first letter of the antibiotic.   
 
Once you have entered the part number and plasmid for your part, you can tab over to the antibiotic resistance field.  The software will automatically fill in the antibiotic resistance based on the plasmid that you have entered.  Please check to make sure that the resistance is correct.  You may change it manually if it is not correct.  The antibiotic abbreviation is the first letter of the antibiotic.   
  
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Please check any of the boxes that apply to your part if it is 1. toxic to Top10 cells, 2. only sending a plasmid, 3. not a part or plasmid.  We need to know specifically whether your part is toxic to Top10 cell strain because it is our standard strain.  We will be transforming all parts into Top10 and we need to know in advance whether this will be a problem with any of your parts.  If you are sending us a plasmid, you need to check the appropriate box (see below for more plasmid information).
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Please check any of the boxes that apply to your part if it is:<br>
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1. toxic to Top10 cells,<br>
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2. only sending a plasmid,<br>
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3. not a part or plasmid<br>
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We need to know specifically whether your part is toxic to Top10 cell strain because it is our standard strain.  We will be transforming all parts into Top10 and we need to know in advance whether this will be a problem with any of your parts.  If you are sending us a plasmid, you need to check the appropriate box (see below for more plasmid information).
  
 
At this point you may add any notes that you may want to communicate with the Registry regarding your part in the comments field.   
 
At this point you may add any notes that you may want to communicate with the Registry regarding your part in the comments field.   
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Once you have finished adding all of the information for your part, click on the “save” link and then “add another sample” button and proceed to filling out all the information as above for each part that you are sending to the Registry.  The information for each sample is automatically saved to this shipment number once you click on the “save” link.   
 
Once you have finished adding all of the information for your part, click on the “save” link and then “add another sample” button and proceed to filling out all the information as above for each part that you are sending to the Registry.  The information for each sample is automatically saved to this shipment number once you click on the “save” link.   
  
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When you are done filling in the information for all of your samples, click on the “I am finished specifying the sample” button. Be aware that your shipment has not yet been finalized (even though it has been saved).  To do so, you must fill in all of your shipping information.  Please provide ALL information.  If you need to obtain a tracking number for your package before finalizing your shipment, you may do so at anytime and come back to finalize your shipment once you have a tracking number. You must provide the shipping details before your information gets sent to the Registry so make sure to come back and complete the shipping details portion of the form. 
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When you are done filling in the information for all of your samples, click on the “I am finished specifying the samples” button. [[Image:Finished_specifying_samples.tiff|300px]] <u>Be aware that your shipment has not yet been finalized (even though it has been saved)</u>.  To do so, you must fill in all of your shipping information.  Please provide ALL information.   
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[[Image:Shipping_details.tiff|350px|center]]
  
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When you are finished providing shipping details, click on the “I am finished filling in this information” button to send your information to the Registry.  This finalizes your shipment information.  You will see a confirmation page that congratulates you on submitting your information.  It will also show all parts that are part of that shipment number.  We recommend printing out this page for your records.   
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If you need to obtain a tracking number for your package before finalizing your shipment, you may do so at anytime and come back to finalize your shipment once you have a tracking number.  You must provide the shipping details before your information gets sent to the Registry so make sure to come back and complete the shipping details portion of the form. 
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When you are finished providing shipping details, click on the “I am finished filling in this information” button to send your information to the Registry.[[Image:Send_to_Registry.tiff|100px]]  
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This finalizes your shipment information.  You will see a confirmation page that congratulates you on submitting your information.  It will also show all parts that are part of that shipment number.  We recommend printing out this page for your records.   
  
 
At this point you can go back to the DNA Submission Registry page and click on “see your DNA submissions” to check on the status of your shipment.  You will be able to see when we have received your shipment and once we have finished testing your parts, you will be able to see the results from our quality control tests.   
 
At this point you can go back to the DNA Submission Registry page and click on “see your DNA submissions” to check on the status of your shipment.  You will be able to see when we have received your shipment and once we have finished testing your parts, you will be able to see the results from our quality control tests.   
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If for any reason we reject your part we will notify you by email (see below for possible reasons your part might be rejected).  The email will be sent to the user who filled out the online submission form.  The rest of the parts in your shipment that passed the quality control tests will be marked as Accepted but you will have to resubmit the parts that did not pass successfully.  These parts must be resubmitted as a new shipment using the online DNA submission form once again.   
 
If for any reason we reject your part we will notify you by email (see below for possible reasons your part might be rejected).  The email will be sent to the user who filled out the online submission form.  The rest of the parts in your shipment that passed the quality control tests will be marked as Accepted but you will have to resubmit the parts that did not pass successfully.  These parts must be resubmitted as a new shipment using the online DNA submission form once again.   
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* Growth in wrong antibiotic broth in antibiotic test
 
* Growth in wrong antibiotic broth in antibiotic test
 
* Wrong fragment size when cut with double restriction enzymes
 
* Wrong fragment size when cut with double restriction enzymes
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Revision as of 13:38, 16 October 2007

[Intro]


Add on Main Page: DNA Requirements (see below)


When you come to the DNA Submission main page, you will be able to “start a new DNA submission” or “see your DNA submissions.” To begin the submission process click on “start a new DNA submission.” File:DNA Submissions main page options.tiff


File:Contact info check.tiff On this page that you must enter information about yourself as the user submitting the DNA. Please make sure that the username and full name that we have listed for you is correct. You then need to choose which team you are on (also called a group). Correct your email if necessary and do not forget to enter your phone number.


You must tell us in what format you are sending your DNA. Choose a format from the drop-down menu and indicate how many samples you are sending. Click here for more information about the accepted formats. You should also let us know if there are any special instructions that we must know about. [IMAGE]



Keep in mind that there are specific DNA amount requirements that you must follow.


For single PCR tube:

  • 20ng in 10ul volume (2ng/ul) minimum needed
  • Wrap tube in lab tape and label with tube number
  • Cap tightly and ship in 50ml Falcon tube


For 8-tube strips:

  • 20ng in 10ul volume (2ng/ul) minimum needed
  • Cap tightly
  • Wrap 1st tube on each 8-tube strip with lab tape and write the correct tube number (e.g. # 1, 9, 17 etc.) with a permanent marker on the tape
  • Ship 8-tube trips inside a 50ml Falcon tube (2 8-tube strips per 50ml Falcon tube)


For 96-well plate:

  • 20ng in 10ul volume (2ng/ul) minimum needed
  • Add DNA to wells in the order of down row 1, down row 2, etc. (i.e. #1 = 1A, #2 = 1B, #3 = 1C, #4 = 1D, #5 = 1E, #6 = 1F, #7 = 1G, #8 = 1H, #9 = 2A, #10 = 2B, etc.)
  • Cover tightly and carefully with aluminum foil adhesive cover (e.g. Axygen PCR-AS-200).


For filter paper grid:

  • Spot at least 160ng DNA onto middle of each square, going down each row in order from left to right (follow the instructions printed on the grid).
  • Fill out the online submission form as well as the paper submission form (with the grid and instructions on how to send the DNA in using this format)
  • Remember to carefully fold the filter paper grid according to the instructions provided on the filter paper.


Proceed to entering sample information by clicking on the button at the bottom of the page. File:Proceed to sample info.tiff


At the top of the sample information page you will see your Shipment #. You will need to remember this number, in particular if you are sending your DNA in filter paper grid format. In this case the shipment # needs to be written clearly on the filter paper grid form.

Begin to enter the information for your first part, beginning with the part number. You must enter the plasmid that the part is in. Note that the software will only recognize plasmids that are documented in the Registry so if you haven’t added your plasmid to the Registry you must do so before submitting your parts. See the “Notes” section below for more details on plasmid information.

Once you have entered the part number and plasmid for your part, you can tab over to the antibiotic resistance field. The software will automatically fill in the antibiotic resistance based on the plasmid that you have entered. Please check to make sure that the resistance is correct. You may change it manually if it is not correct. The antibiotic abbreviation is the first letter of the antibiotic.

Please check any of the boxes that apply to your part if it is:
1. toxic to Top10 cells,
2. only sending a plasmid,
3. not a part or plasmid

We need to know specifically whether your part is toxic to Top10 cell strain because it is our standard strain. We will be transforming all parts into Top10 and we need to know in advance whether this will be a problem with any of your parts. If you are sending us a plasmid, you need to check the appropriate box (see below for more plasmid information).

At this point you may add any notes that you may want to communicate with the Registry regarding your part in the comments field.

Once you have finished adding all of the information for your part, click on the “save” link and then “add another sample” button and proceed to filling out all the information as above for each part that you are sending to the Registry. The information for each sample is automatically saved to this shipment number once you click on the “save” link.

When you are done filling in the information for all of your samples, click on the “I am finished specifying the samples” button. File:Finished specifying samples.tiff Be aware that your shipment has not yet been finalized (even though it has been saved). To do so, you must fill in all of your shipping information. Please provide ALL information. File:Shipping details.tiff

If you need to obtain a tracking number for your package before finalizing your shipment, you may do so at anytime and come back to finalize your shipment once you have a tracking number. You must provide the shipping details before your information gets sent to the Registry so make sure to come back and complete the shipping details portion of the form.

When you are finished providing shipping details, click on the “I am finished filling in this information” button to send your information to the Registry.File:Send to Registry.tiff

This finalizes your shipment information. You will see a confirmation page that congratulates you on submitting your information. It will also show all parts that are part of that shipment number. We recommend printing out this page for your records.

At this point you can go back to the DNA Submission Registry page and click on “see your DNA submissions” to check on the status of your shipment. You will be able to see when we have received your shipment and once we have finished testing your parts, you will be able to see the results from our quality control tests.


If for any reason we reject your part we will notify you by email (see below for possible reasons your part might be rejected). The email will be sent to the user who filled out the online submission form. The rest of the parts in your shipment that passed the quality control tests will be marked as Accepted but you will have to resubmit the parts that did not pass successfully. These parts must be resubmitted as a new shipment using the online DNA submission form once again.

Reasons for failing quality control:

  • Failed to transform
  • Did not grow in culture
  • Growth in wrong antibiotic broth in antibiotic test
  • Wrong fragment size when cut with double restriction enzymes



Notes:

  • Accepting bacteria
    • The Registry will accept bacteria if you absolutely cannot send miniprepped DNA. You must still complete the online submission form (both the sample information and the shipping details). Note that if you choose to send your parts as bacteria, there will be a delay in the time it takes for your shipment to go through the quality control process. Also, please do not write E. coli on your shipment information as the U.S. has had some issues with E. coli outbreaks and this will likely delay delivery of your package to the Registry.
  • Editing your shipment after it has been finalized
    • You may edit your shipment at any point up until the time you finalize your shipment after entering your shipping details. After you have finalized your shipment and sent all parts and information to the Registry, you will not be able to edit your online submission form. If you need to make a change to your submission form information, you must contact Meagan Lizarazo at meaganl [at] mit [dot] edu. Please include your shipment number, your name, your team name, and the sample information that you would like to change.
  • Part and plasmid specification details
    • In specifying your parts you must clearly understand the relationship between parts and plasmids. You must be explicitly aware that a part does NOT include the flanking restriction enzyme sites (called BioBrick prefix and suffix if you are using the BioBrick™ standard for which the restriction enzymes are: EcoRI, XbaI, SpeI, PstI). These sites must instead be specified in the plasmid that your part is in. Your part, then, begins with the first letter (A, C, T, G) following the prefix cloning site of the plasmid and ends with the last letter preceding the suffix cloning site of the plasmid.
    • One of the reasons the Registry needs to know exactly what the details are for the plasmid your part is in is so that we can use the correct set of enzymes for our digest portion of the quality control process. We need to be able to calculate the length of your part when cut with that particular set of restriction enzymes (especially if is a set of restriction enzymes different than those of the BioBrick™ standard. The plasmid information must also have the antibiotic resistance markers that are part of the plasmid. This information is also extremely important for the quality control testing.