2026-2027 WSSP Lecture Notes, Presentations, and Videos
This web page provides links to materials for the Waksman Student Scholars Program for the 2026-2027 Summer Institutes and Academic Year programs. This information is intended for the students and faculty participating in the program during the 2026 Summer Institute and through the 2026-2027 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. | 2026-2027 Lecture Topics Student Links |
Notes |
Videos (.mp4) |
Figures (.pdf) |
Figures (.ppt) |
|---|---|---|---|---|---|
| Introduction and overview of project | Ch0 | Ch.0.pdf | Ch0.ppt | ||
| 0 | Review of DNA Structure, Transcription, Translation | Ch0 | Ch0.pdf | Ch0.ppt | |
| 1 | Vectors: Plasmids, Libraries, and DNA preps (full chapter) A) Background on Vectors B) Background on Libraries C) Plasmid DNA Minipreps |
Ch1 Ch1A Ch1B Ch1C |
Ch1A Ch1B Ch1C |
Ch1.pdf |
|
| 2 | PCR, Mapping the size of an insert (full chapter) A) Background on PCR B) Analysis of an agarose gel of the PCR samples |
Ch2 Ch2A Ch2B |
Ch2A Ch2B |
Ch2.pdf | Ch2.ppt |
| 3 | Restriction enzymes, Mapping the size of an insert (full chapter) A) Background on Restriction Enzymes B) Analysis of an agarose gel of the Restriction Digest samples |
Ch3 Ch3A Ch3B |
Ch3A Ch3B |
Ch3.pdf | Ch3.ppt |
| 4 | DNA Sequencing | Ch4 | Ch4 | Ch4.pdf | Ch4.ppt |
| 5 | DSAP, Sequence quality, crop ends (full chapter) A) Bioinformatic Analysis Overview A1) DSAP Overview B) Determine waveform quality C) Analysis of a poor waveform D) Cropping the waveform Q2: Insert Start Q3: Insert End Q4: Crop Sequence E) Editing the waveform |
Ch. 5 Ch5A Ch5B Ch5E |
Ch5A0 Ch5A1 Ch5B Ch5C Ch5Di Ch5Dii Ch5Diii Ch5E |
Ch5.pdf | |
| 6 | BLASTN (DNA vs DNA search) (full chapter) A) Performing a BLASTn seach of ClusteredNR database B) Analyzing the NCBI BLASTn i) Analysis of Matches ii) BLASTN Analysis of Alignment iii) BLASTn searches: Fill in Tables C) BLASTN of the EST database |
Ch6 Ch6A Ch6B Ch6Bii Ch6C |
Ch6A Ch6Bi Ch6Bii Ch6Biii Ch6C |
Ch6.pdf | Ch6.ppt |
| 7 | BLASTX (Translated DNA vs Protein search) (full chapter) A) BLASTx Background B) Performing a BLASTx seach C) Analysis of BLASTX Alignments D) Analysis of BLASTX Results: Does the DNA code for a protein? E) Analysis of BLASTX Results: Frameshifts |
Ch7A Ch7B Ch7C Ch7D Ch7E |
Ch7.pdf | Ch7.ppt | |
| 8 | ORFs, BLASTP (Protein vs Protein search) (full chapter) A) Overview of ORF Determination, BLASTP, UTRs B) Using Toolbox to Determine the ORF C) Performing the BLASTP search D) Comparison of the BLASTX vs BLASTP data |
Ch8 Ch8A Ch8B Ch8C Ch8D |
Ch8A Ch8B Ch8C Ch8D |
Ch8.pdf | Ch8.ppt |
| 9 | Determining Ranges (full chapter) | Ch9 | Ch9 | Ch9.pdf | Ch9.ppt |
| 10 | Protein Information (full chapter) A) Literature Search B) Search for a human homolog C) PDB Search for Homologous Proteins |
Ch10 Ch10A Ch10B Ch10C |
Ch10A Ch10B Ch10C |
Ch10.pdf | Ch10.ppt |
| 11 | DNA Sequence Information (full chapter) A) Compare Insert Sizes (Only if you purified your own clones) B) Next Gen Sequencing and TSA Search -i) Background ii) BLASTN of TSA and BLASTX with Contig |
Ch11 Ch11A Ch11B Ch11C |
Ch11A Ch11Bi Ch11Bii |
Ch11.pdf | Ch11.ppt |
| 12 | Arabidopsis Homologs (full chapter) A) Model Systems B) NCBI BLASTp search for Arabidopsis Homologs C) Protein Interactions Background Search of the BioGRID Database: Steps D) Expression Analysis Expression Studies on the eFP Browser E) Localization Localization Studies on the Cell efP Browser |
Ch12 Ch12A Ch12B Ch12C Ch12D Ch12E |
Ch.12 Ch12A Ch12B Ch12C Ch12D Ch12E |
Ch12.pdf | Ch12.ppt |
| 13 | What experiments to do next (full chapter) | Ch13 Ch13A Ch13B |
Ch.13A Ch.13B |
Ch13.pdf | Ch.13.ppt |
| 14 | Preparing a poster | Ch21.ppt |
Download FinchTV (Mac or PC- external site)
SnapGene (Mac or PC)