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2020-2021 WSSP Lecture Notes, Presentations, and Videos

This web page provides links to materials for the Waksman Student Scholars Program for the 2020-2021 academic year. This information is intended for the students and faculty participating in the program during the 2020 Summer Institute and through the 2020-2021 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 not a member of the WSSP and wish to download the files or have comments or questions about the material please contact Sue Coletta, Waksman Institute, Rutgers University.

Ch. 2020Lecture Topics Student Links
 

Notes 
(.pdf)

Videos
(.mp4)
Figures 
(.pdf)
Figures 
(.ppt)
0
Introduction and overview of project   Ch0
0
Polymers and DNA Structure    
1
Vectors: Plasmids, Libraries, and DNA preps
   Background on Vectors
   Background on Libraries
   Plasmid DNA Minipreps
 
Ch.1A
Ch.1B
Ch.1C
2
PCR, Mapping the size of an insert
   Background on PCR
   Analysis of an agarose gel of the PCR samples
 
Ch.2A
Ch.2B
3
Restriction enzymes, Mapping the size of an insert
   Background on Restriction Enzymes
   Analysis of an agarose gel of the Restriction Digest samples
 
Ch.3A
Ch.3B
4
DNA Sequencing,   Ch.4
5
Logging onto DSAP, Sequence quality, crop ends
   DSAP & Bioinformatic Analysis Overview  
   Determine waveform quality
   Analysis of a poor waveform
   Cropping the waveform
 
Ch.5A
Ch.5B
Ch.5C
Ch.5D

Ch5.ppt

6
Editing the waveform Ch.6
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.7A
Ch.7B
Ch.7C
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
9
Determining ORFs, BLASTP (Protein vs Protein search)
  Overview of ORF Determination, BLASTP, UTRs
  Using Toolbox to Determine the ORF
  Performing the BLASTP search
  Comparison of the BLASTX vs BLASTP data
  Review Page: Determining the 5' and 3' UTRs
Ch.9A
Ch.9B
Ch.9C
Ch.9D
Ch.9E
10
Literature Search Ch.10
11A Search for a human homolog Ch.10B Ch.11(A)    
11B
Compare Insert Sizes (Only if you purified your own clones) Ch.11
12
PDB Search for Homologous Proteins

 

Ch.12 
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
   Steps
Ch. 14  
Ch.14A
Ch.14B
Ch14.pdf Ch14.ppt
15 Expression and Localization Analysis
   Analysis of the Expression Studies
   Analysis of the Localizatino Studies
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.18a
Ch.18b
Ch.18c

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

Parental Release Form (doc) (pdf)

Download FinchTV (external site)   Download FinchTV (from WSSP site)

Download 4Peaks 

List of DNA Sequence Waveform Viewers can be found here