CTR:Protocols: Difference between revisions

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Replace this sentence with a brief description of the protocol and its goal.
Replace this sentence with a brief description of the protocol and its goal.
To be edited!
To be edited!
==Beckman Sequencing==
PCR product: 20μL. Primer: 25μL of 3μM
# Go to https://psf.beckmangenomics.com/ and login
# Select "Create New Project" at top left
# Select "Single Pass PCR Sequencing" under High Throughput Sequencing - Other
# Enter "Project Name" (distinct to this plate, e.g. Lori_Africa09_1)
# Enter how many plates of PCR products you are sending under "Sample Format"
# Enter "Amplicon size"
# Select No under "Are your samples purified"
# Fill out "Sequencing Requirements" (e.g. if you are sending one plate with two directions, total will be 192)
# Click Next
# Download the template under "Primer Information" ("singlepasspcr_primer_template.xls")
# Under "Sample Information" enter plate name, amount (20μL) & amplicon size. Under "Primer Information" enter plate name, amount (25μL), & conc. (3μM)
# Upload the template by clicking "Attach File"
# Click Next
# Next page is pretty self explanatory. Choose ".ab1" under "Data Delivery"
# Click Next
# Enter Purchase Order # info (on back of computer room door)
# Click Next
# Confirmation. You will need to include this page with the shipment.
To Ship:
# Login to [http://www.fedex.com/us/ FedEx account]
# Create Shipment
# Under "Company" in the "TO" fields, start typing Beckman. The address should pop up. if not:
Beckman Coulter Genomics
<br>Attn: Genomic Services
<br>36 CHERRY HILL DR
<br>DANVERS, MA 019232575
<br>(800)361-7780
# Choose Standard Overnight in the "Service Type" under "3. Package and shipment details"
# Ball park estimate the weight with dry ice
# Select Your Packaging
# On the right hand side, Click "Edit" by "Special Services"
# Select Dry Ice and Deliver without Signature under "Signature type"
# Click Ship at bottom of page
# Confirm Details and Ship
# Print Shipping Label
# Pack up box with plates and dry ice (buffer plates a little so they don't shatter). Be sure to fill out and include the dry ice label on the box (available at the storeroom). Stick this on LAST, after the box has been sealed.
# Last pickup at storeroom is around 3:30pm
Notes:
*For getting dry ice from the store room, remember to fill out the card with the recharge ID. Only whole numbers in pounds are accepted. For example, you can get 1 or 2 pounds of dry ice, but not 1.5.
*To ship with dry ice, remember that the styrofoam box with your contents must be in a cardboard box.
*Remember to deduct the total from the signup sheet on the computer room door.


==Printing field labels==
==Printing field labels==
Line 16: Line 63:
# Save the file.
# Save the file.


==Procedure==
# In a PCR tube, mix the components on ice in the order they are listed above.
# Perform thermocycling program
## 95 °C 5 min
## 95 °C 30 s
## T<sub>H</sub> 30 s
## 72 °C 1 min for each 1 kb PCR product
## Repeat steps 2-4 a total of 12-36 times (24 is standard).
## 72 °C 5 min
## 12 °C hold
==Notes==
Please feel free to post comments, questions, or improvements to this protocol. Happy to have your input!
#List troubleshooting tips here. 
#You can also link to FAQs/tips provided by other sources such as the manufacturer or other websites.
#Anecdotal observations that might be of use to others can also be posted here. 


Please sign your name to your note by adding <font face="courier"><nowiki>'''*~~~~''':</nowiki></font> to the beginning of your tip.
==placeholder==
'''placeholder'''


==References==
'''Relevant papers and books'''
<!-- If this protocol has papers or books associated with it, list those references here.-->
<!-- See the [[OpenWetWare:Biblio]] page for more information, but this format doesn't work currently.
<biblio>
#Goldbeter-PNAS-1981 pmid=6947258
#Jacob-JMB-1961 pmid=13718526
#Ptashne-Genetic-Switch isbn=0879697164
</biblio>-->
<!-- Try the [[Template:FormatRef|FormatRef template]]-->
#{{FormatRef|Goldbeter, A and Koshland, DE|1981| |Proc Natl Acad Sci U S A 78(11)|6840-4| }} PMID 6947258
#{{FormatRef|Jacob, F and Monod, J J|1961| |Mol Biol 3(3)|318-56| }} PMID 13718526
#{{FormatRef|Ptashne, M|2004|Genetic Switch: Phage Lambda Revisited| | |Cold Spring Harbor Laboratory Press}} ISBN 0879697164


==Contact==
*Who has experience with this protocol?


or instead, [[Talk:{{PAGENAME}}|discuss this protocol]].


<!-- You can tag this protocol with various categories.  See the [[Categories]] page for more information. -->
<!-- You can tag this protocol with various categories.  See the [[Categories]] page for more information. -->

Revision as of 12:55, 6 May 2014

Overview

Replace this sentence with a brief description of the protocol and its goal. To be edited!

Beckman Sequencing

PCR product: 20μL. Primer: 25μL of 3μM

  1. Go to https://psf.beckmangenomics.com/ and login
  2. Select "Create New Project" at top left
  3. Select "Single Pass PCR Sequencing" under High Throughput Sequencing - Other
  4. Enter "Project Name" (distinct to this plate, e.g. Lori_Africa09_1)
  5. Enter how many plates of PCR products you are sending under "Sample Format"
  6. Enter "Amplicon size"
  7. Select No under "Are your samples purified"
  8. Fill out "Sequencing Requirements" (e.g. if you are sending one plate with two directions, total will be 192)
  9. Click Next
  10. Download the template under "Primer Information" ("singlepasspcr_primer_template.xls")
  11. Under "Sample Information" enter plate name, amount (20μL) & amplicon size. Under "Primer Information" enter plate name, amount (25μL), & conc. (3μM)
  12. Upload the template by clicking "Attach File"
  13. Click Next
  14. Next page is pretty self explanatory. Choose ".ab1" under "Data Delivery"
  15. Click Next
  16. Enter Purchase Order # info (on back of computer room door)
  17. Click Next
  18. Confirmation. You will need to include this page with the shipment.

To Ship:

  1. Login to FedEx account
  2. Create Shipment
  3. Under "Company" in the "TO" fields, start typing Beckman. The address should pop up. if not:

Beckman Coulter Genomics
Attn: Genomic Services
36 CHERRY HILL DR
DANVERS, MA 019232575
(800)361-7780

  1. Choose Standard Overnight in the "Service Type" under "3. Package and shipment details"
  2. Ball park estimate the weight with dry ice
  3. Select Your Packaging
  4. On the right hand side, Click "Edit" by "Special Services"
  5. Select Dry Ice and Deliver without Signature under "Signature type"
  6. Click Ship at bottom of page
  7. Confirm Details and Ship
  8. Print Shipping Label
  9. Pack up box with plates and dry ice (buffer plates a little so they don't shatter). Be sure to fill out and include the dry ice label on the box (available at the storeroom). Stick this on LAST, after the box has been sealed.
  10. Last pickup at storeroom is around 3:30pm

Notes:

  • For getting dry ice from the store room, remember to fill out the card with the recharge ID. Only whole numbers in pounds are accepted. For example, you can get 1 or 2 pounds of dry ice, but not 1.5.
  • To ship with dry ice, remember that the styrofoam box with your contents must be in a cardboard box.
  • Remember to deduct the total from the signup sheet on the computer room door.


Printing field labels

  1. Create Excel sheet listing all field numbers. Save as 1997-2003 Excel format and transfer to flash drive or send in email.
  2. On Nanodrop computer, log on to "General" account.
  3. Open BarTender program. Open an older file to edit as a template or start a new one.
  4. Go to "Database Connection Setup". Select the Excel sheet with the field numbers.
  5. Edit the label as necessary.
  6. Print label.
    1. First click "Test Print". This will print the first entry in the Excel sheet.
    2. If the label looks fine, enter the field number range in "Selected Records" (for example, 1-200). Recommend printing no more than 100-200 at a time to ease organization and to check for toner fading.
  7. Save the file.


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