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Lecture Notes for Students 2024

2024-2025 WSSP Lecture Notes, Presentations, and Videos

This web page provides links to materials for the Waksman Student Scholars Program for the 2024-2025 Summer Institutes and Academic Year programs. This information is intended for the students and faculty participating in the program during the 2023 Summer Institute and through the 2023-2024 academic year. It is not intended for general public use and access is password protected. The material on these pages is provided for educational purposes only. Unauthorized use of this material is prohibited.
If you are participating in the WSSP, and can not access the files, ask your teacher for the password.  NOTE: There is a new password this year.
If you are not a member of the WSSP and wish to download the files or have comments or questions about the material please contact wssp@waksman.rutgers.edu.  

Ch. 2024-2025 Lecture Topics Student Links
 

Notes 
(.pdf)

Videos
(.mp4)
Figures 
(.pdf)
Figures 
(.ppt)
0 Introduction and overview of project   Ch0 Ch.0.pdf Ch.0.ppt
0 Polymers and DNA Structure     Ch0.pdf Ch0.ppt
1 Vectors: Plasmids, Libraries, and DNA preps
   Background on Vectors
   Background on Libraries
   Plasmid DNA Minipreps
Ch. 1  
Ch.1A
Ch.1B
Ch.1C
Ch1.pdf

 

2 PCR, Mapping the size of an insert
   Background on PCR
   Analysis of an agarose gel of the PCR samples
Ch. 2  
Ch.2A
Ch.2B
Ch2.pdf Ch2.ppt
3 Restriction enzymes, Mapping the size of an insert
   Background on Restriction Enzymes
   Analysis of an agarose gel of the Restriction Digest samples
Ch. 3  
Ch.3A
Ch.3B
Ch3.pdf Ch3.ppt
4 DNA Sequencing,   Ch. 4 Ch.4 Ch4.pdf Ch4.ppt
5 Logging onto DSAP, Sequence quality, crop ends
   DSAP & Bioinformatic Analysis Overview  
   Determine waveform quality
   Analysis of a poor waveform
   Cropping the waveform
Ch. 5  
Ch.5A
Ch.5B
Ch.5C
Ch.5D
Ch5.pdf

Ch5.ppt

6 Editing the waveform Ch. 6 Ch.6 Ch6.pdf Ch6.ppt 
7 BLASTN (DNA vs DNA search)
   Q1a. Performing a BLASTn seach of nr
   Q1b. Analyzing the NCBI BLASTn results
   Q2-5. DSAP tables on the BLASTn searches
Ch. 7   
Ch.7A
Ch.7B
Ch.7C
Ch7.pdf Ch7.ppt
8 BLASTX (Translated DNA vs Protein search)
   BLASTx Background
   Q1-4. Performing a BLASTx seach on the NCBI nr database
   Analysis of Frameshifts

 

 
Ch.8A
Ch.8B
Ch.8C
Ch8.pdf Ch8.ppt
9 Determining ORFs, BLASTP (Protein vs Protein search)
  Overview of ORF Determination, BLASTP, UTRs
  Using Toolbox to Determine the ORF
  Using NCBI ORFfinder to Determine the ORF
  Performing the BLASTP search
  Comparison of the BLASTX vs BLASTP data
  Review Page: Determining the 5' and 3' UTRs
Ch. 9 Videos
Ch.9A
Ch.9B1
Ch.9B2
Ch.9C
Ch.9D
Ch.9E
Ch9.pdf Ch9.ppt
10A Literature Search Ch.10A Ch.10A Ch10A.pdf Ch10A.ppt
10B Search for a human homolog Ch.10B Ch.10B Ch10B.pdf Ch10B.ppt
11 Compare Insert Sizes (Only if you purified your own clones) Ch. 11 Ch.11 Ch11.pdf Ch11.ppt
12 PDB Search for Homologous Proteins

Ch. 12

Ch.12  Ch12.pdf Ch12.ppt
13 Next Gen Sequencing and TSA Search
   Background
   Steps
Ch. 13  
Ch.13A
Ch.13B
Ch13.pdf Ch.13.ppt
14 Searching for Protein Interactions
   Background
   TAIR or NCBI BLASTp search for Arabidopsis Homologs
   Search of the BioGRID Database: Steps
Ch. 14  
Ch.14A
Ch.14B
Ch.14C
Ch14.pdf Ch14.ppt
15 Expression and Localization Analysis
   Expression Studies on the eFP Browser
   Localization Studies on the Cell efP Browser
Ch. 15 Ch.15A
Ch.15B
Ch15.pdf Ch15.ppt
16 Molecular Biology Expts.:  What to do next Ch. 16 Ch.16A
Ch.16B
Ch16.pdf Ch16.ppt
17 Multiple Sequence alignment CLUSTALW (optional) Ch. 17   Ch17.pdf Ch17.ppt
18 Analysis of REV sequences (optional)
   Rev Sequence Quality
   Rev Sequence Insert Start
   Rev Sequence Insert End
Ch. 18

 

Ch18.pdf Ch18.ppt
19 Spanning the gap (optional) Ch. 19   Ch19.pdf Ch19.ppt
20 JMol and Protein Modeling (optional) Ch. 20   Ch20.pdf Ch20.ppt
21 Preparing a poster  (optional)    

Ch21.pdf

Ch21.ppt

Parental Release Form https://form.jotform.com/221795511773158 

Download FinchTV (Mac or PC- external site)   

Download 4Peaks 

SnapGene (Mac or PC)

MY SEQUENCE (Apple App for iPads,  Phones.  This can also be used in place of Toolbox.)

List of DNA Sequence Waveform Viewers can be found here