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Supplies

***Please note that for the 2019-2020 Academic Year we are requesting that schools purchase pipets, tips, and tubes for all of their students to conduct the project at their schools. To help schools determine how much of each supply they will need, along with the costs, we have created a Supply Calculation spread sheet.  Please let us know  if you have any questions about the spread sheet or which items to order.

The 2019 WSSP will provide reagents, supplies, sequencing and review for the first two rounds of clones prepared by each student at participating schools. Schools that wish to have students analyze Additional clones will need to purchase materials for the analysis and pay for the costs of sequencing, posting, reviewing and submitting the Additional clone sequences to NCBI.  Below is our Policy for doing Additional clones.  

WSSP Policy for doing Additional clones during the 2019-2020 Academic Year

1. The WSSP will provide the cDNA library plates and primers for school Teams that decide to conduct the Additional experiments.  As is customary, requests for cDNA library plates require 2 weeks advance notice.

2. Participating schools will provide all other supplies and reagents that are required to conduct the Additional wet laboratory experiments.  See the table and notes below for suggested materials and vendors.

3. All gel pictures and data about the Additional clones must be posted on the school’s Google Docs Clone Report Sheet.  Each school is responsible for determining if their Additional clones are adequate for sequencing and should indicate this on their Google Docs Clone Report Sheet.

4. After posting gel pictures and data on the school’s Google Docs Clone Report Sheet, the plasmid DNA minipreps should then be sent to the WSSP project staff at the Waksman Institute, Rutgers University, Piscataway, NJ, where they will be processed for sequencing by Macrogen.  Please Note:  To reduce costs, clones will not be sent out individually for sequencing but will be batched with other project clones until there is a full tray. 

5. The WSSP staff will post and review the sequences obtained from the Additional clones. After these sequences are fully vetted by WSSP staff, they will be submitted by the project staff to NCBI. Please Note:  The WSSP is not responsible for poor quality sequences or sequences that cannot be submitted to NCBI.

6. The cost associated with the support provided by the WSSP for Additional clones (processing, sequencing, reviewing, and posting on NCBI) will be $12.50/clone.  The cost associated with a reverse sequence for a vetted clone (as described above) will be an additional $12.50/clone.  Schools will be invoiced for the services that are associated with analyzing Additional clones after the plasmid DNA minipreps are received by the WSSP staff (Step 4), but before these sequences are posted on DSAP (Step 5).

Below is a list of supplies that are used in the summer Institutes and academic year program to conduct the molecular biology research project that is part of the WSSP.  Most of the supplies used by the WSSP have been purchased through VWR because the company provides Rutgers University with discounted prices. Other vendors may have similar supplies. We strongly recommend that you shop around for the best deal.  Some vendors may offer donations, so we suggest you call a supplier first, and explain the project.  

Reagents and Supplies Used in the WSSP Project 

Experiment #/clone  VWR Genesee Edvotech Carolina BioExpress BioRad Invitrogen NEB Qiagen Promega 
Culture Supplies
  10 ml Serological pipets, Individually wrapped1 1 89130-898 12-104     P-2837-10          
  10 ml Serological pipets, bulk bag1 1 89130-910 12-112     P-2820-11          
  17X100 Polstyrene sterile culture tubes 1 60818-725 21-129   215090 T-2841-4          
  Miller's LB  solid (make up liquid)2 2 ml 97064-108 11-120 616 216700 MBPE-2020          
  Millers LB  (in liquid form) 2 ml 101384-874   611 216650 G-3258-1000          
  cDNA Library Plates - Provided by WSSP 1 colony                    
  Ampicillin - Provided by WSSP .002 ml 97061-442     216858            
  Innoculating Loops Sterile3 1 60820-132     215850 J-5112-4          
 
Miniprep Supplies
  Microifuge tubes, clear (MP, digests, PCR, gels)4 5.5 20170-333 24-282   215230 C-3260-1 223-9501        
  Microifuge tubes, yellow (for MP DNA) 1 20170-335       C-3260-Y          
  1-200 ul yellow tips (MPs, digest, PCR, gels)4 22 53509-010 24-151R   215051 P-1231-200 223-9303        
  100-1000 ul Blue tips (minipreps) 4 83007-378 24-161R   215061 P-1231-1000 223-9350        
  1-200 ul tips, reloads   53509-012 24-151RL     P-1235-200          
  100-1000 ul tips, reload   89003-422 24-161RL     P-1235-1000          
  Illustra plasmid Prep Mini Spin Kit4 1 prep 95026-748 83-594                
  Plasmid Miniprep-Classic Kit 1 prep 97064-828 11-308A       732-6400EDU     27104 A1223
  Ethanol (required for Miniprep kits)           BDH1160-4LP          
  PvuII-HF Enzyme 1 ul               R3151S    
  PvuII5 1 ul 101228-826                  
 
PCR Supplies 7
  Illustra Ready to-Go PCR beads 0.2 ml tube w cap 1 89497-136 84-867                
  Primers - Provided by the WSSP
  Taq master Mix8 12.5 ul 30035-1 42-131 625   C-5052-1 166-5009EDU        
  PCR Tubes , 0.2 ml flat cap 1 89511-270 24-154 642.2 215242 C-3328-1 TFI0201        
 
Agarose gel Supplies
  Agarose (assuming 8 samples/gel) .15 g 12001-870 20-101 605-100 217080 E-3119-500 161-3100EDU        
  TAE 50X, liquid 20 ml 97063-692 20-193 607XL 219033 MRGF-4210 161-0743EDU        
  TAE 50X, solid   97062-518       0912-2          
  DNA Sizing ladder (Rec Invitrogen9) 20 ul 95057-692 19-111 750       10787-026      
  Loading Dye 5 ul 470105-014   606 218200 K945-5ML 166-0401EDU        
  Powder Free Nitrile gloves 2 32916-670 44-100 774 706335 G-4048          
  DNA Stain - Gel Red or green    89139-134     217305 89139-138 166-5111EDU        
  Ethidium Bromide- provided by WSSP if can use       2001 217422   161-0433EDU        

FootNotes:

1. If students are working in groups of four then one pipet can be used to dispense 2.0 ml of LB to 4 tubes.

2. Because many schools do not have access to an autoclave we suggest that schools purchase sterilized LB liquid to grow their Additional cultures.  However, to save costs, instead of purchasing liquid LB it is possible to purchase LB powder and make up the liquid LB in batches.  This can be done by either filter sterilization (which is expensive) or the LB can be sterilized by heating in a microwave to boiling and cooling three times.  After the final cooling, the ampicillin can be added to the LB and stored in the refrigerator. 

3.  Instead of the sterile disposable sticks, it is possible to buy disposable sterile plastic inoculation loops.  Alternatively, metal inoculation loops can be sterilized using Bunsen burners, which can then be used to inoculate the culture.

4. This is the number of tips or tubes that is required for all of the Additional experiments: PCR, DNA minipreps, restriction digests, and agarose gel electrophoresis.  

5. The WSSP currently uses Qiagen Plasmid Miniprep Kits to purify the plasmid DNA. You may find less expensive alternatives from other vendors. If you do buy other kits please note the differences in the volumes used for each of the solutions and do not use one set of solutions for another column.

6. The WSSP supplies PvuII-HF from New England BioLabs for the first two rounds.  It is strongly suggested that schools purchase the same enzyme for conducting the restriction digests on the Additional clones they analyze.  If regular PvuII is purchased from NEB please note that it uses a different buffer!! Please take care to not swap the different buffers with the different enzymes. 

7. To save costs, schools may want to omit the PCR screen of the clones.  This will save on PCR reagents and one round of agarose gels.  The restriction digest will provide the information on the size of the insert, as well as the quality of the DNA prep.

8. In the past, the WSSP used GE Illustra RTG PCR Beads for the PCR. You may find considerably less expensive alternatives, such as using a Taq mix that is available from other vendors. The Taq mix is usually a 2X mix that contains the PCR buffer, Taq enzyme, and dNTPs for the reaction.  Two words of caution if you use the Taq mix: 1) Be sure students use the correct size pipetor when they aliquot the mix;  2) Make sure the students do not add anything to the stock tube of the Taq Mix.

9. For consistency, we strongly recommend that schools use the 1 KB DNA ladder marker from Invitrogen for the agarose gel analysis of their Additional clones.  If schools do purchase other markers, then please only use them for the analysis of the Additional clones.  Gels of the clones from the first two rounds (that are supported by the program) with non-standard markers can not be reviewed by the WSSP staff.