2022-2023 WSSP Lecture Notes, Presentations, and Videos
This web page provides links to materials for the Waksman Student Scholars Program for the 2022-2023 academic year. This information is intended for the students and faculty participating in the program during the 2022 Summer Institute and through the 2022-2023 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. | 2022-2023 Lecture Topics Student Links |
Notes |
Videos (.mp4) |
Figures (.pdf) |
Figures (.ppt) |
|---|---|---|---|---|---|
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0
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Introduction and overview of project | Ch0 | |||
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0
|
Polymers and DNA Structure | ||||
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1
|
Vectors: Plasmids, Libraries, and DNA preps Background on Vectors Background on Libraries Plasmid DNA Minipreps |
Ch.1A Ch.1B Ch.1C |
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2
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PCR, Mapping the size of an insert Background on PCR Analysis of an agarose gel of the PCR samples |
Ch.2A Ch.2B |
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3
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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 |
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4
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DNA Sequencing, | Ch.4 | |||
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5
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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 |
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6
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Editing the waveform | Ch.6 | |||
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7
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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 |
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8
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BLASTX (Translated DNA vs Protein search) BLASTx Background Q1-4. Performing a BLASTx seach on the NCBI nr database Analysis of Frameshifts |
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Ch.8A Ch.8B Ch.8C |
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9
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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 |
Videos Ch.9A Ch.9B1 Ch.9B2 Ch.9C Ch.9D Ch.9E |
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10A
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Literature Search | Ch.10A | |||
| 10B | Search for a human homolog | Ch.10B | Ch.10B | Ch10B.pdf | Ch10B.ppt |
|
11
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Compare Insert Sizes (Only if you purified your own clones) | Ch.11 | |||
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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 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 |
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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 https://form.jotform.com/221795511773158
Download FinchTV (Mac or PC- external site) Download FinchTV (from WSSP site)
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