Biomedical Sciences Program - University of California San Diego (UCSD)
Instructor: Emily Wheeler (ecwheele@ucsd.edu)
Instructor: Ryan Marina (rmarina@ucsd.edu)
Lecturer: Dave Gorkin (dgorkin@ucsd.edu)
Lecturer: Eric Van Nostrand (elvannostrand@ucsd.edu)
Lectures will all be held in CMME room 2047. See below for daily schedule.
| Day | Date | Time | Topic | Lecture |
|---|---|---|---|---|
| 0 | Pre-CLASS | Setup TSCC accounts | ||
| Wednesday | 9/27/17 | 9A - 1P | Sequencing Applications Lecture (Dave Gorkin) and Intro to Unix | |
| Thursday | 9/28/27 | 9A - 1P | Downloading Data, Fastqc, Alignment | |
| Friday | 9/29/17 | 9A - 1P | Alignment Recap, Samtools, Gene Quantification | |
| Monday | 10/2/17 | 9A - 1P | Jupyter Notebooks, DESeq2 | |
| Tuesday | 10/3/17 | 9A - 1P | RNA Applications Lecutre (Eric Van Nostrand) and Python Demo | |
| Wednesday | 10/4/17 | 9A - 1P | Gene Pattern |
| Day | Date | Time | Location | Hosting |
|---|---|---|---|---|
| Thursday | 9/28/27 | 4P - 6P | The Lounge (old Cafe Vita) | Ryan M |
| Sunday | 10/1/17 | 1P - 3P | Mesa Nueva (Cresta Study Rooms) | Emily + Krystyna |
| Tuesday | 10/3/17 | 6P - 8P | SCRM meetings | Emily |
| Thursday | 10/5/17 | 3P - 5P | Leichtag Lobby | Josh + Ryan G |
| Sunday | 10/8/17 | 1P - 3P | Mesa Nueva | Krystyna |
Group Assignments
| Group 1 | Group 2 | Group 3 | Group 4 | Group 5 | Group 6 |
|---|---|---|---|---|---|
| Helen | Spencer | Matthew | Dominic | Tom | Erin |
| Derrick | Bernadette | Josh B. | Alex | Gabby | Melinda |
| Celeste | Margaret | Juan | Ryan | Phoebe | Carter |
| Josh L. | Brian | Rebecca | Alanna | Yilan | Noor |
| Ila | Tiani | Emily |
Location: SCRM 3116 (across from elevator on 3rd floor)
Date: Tuesday October 3
| Time | Group |
|---|---|
| 6:00 - 6:20 | Group 2 |
| 6:20 - 6:40 | Group 6 |
| 6:40 - 7:00 | Group 1 |
| 7:00 - 7:20 | Group 3 |
| 7:20 - 7:40 | Group 4 |
| 7:40 - 8:00 | Group 5 |
Proposal
-
Assigned Friday 9/29
-
Due to Emily and Ryan via email Sunday 10/1 at 11:59 PM
-
Work together on your teams to generate an interesting biological question that can be answered with publically available datasets. You can use the ENCODE website, or other sources that you find. You can even use things that have been published and uploaded to the GEO repository, we will help you download any datasets that you find particularly interesting!
-
Your question must incorporate the integration of data from two different assays, one of which must be RNA-Seq, and the second must be something other than RNA-Seq (CHIP-Seq, CLIP-Seq, ATAC-Seq, exome sequencing, genome sequencing). The RNA-Seq must have at least two conditions and two replicates per condition (3 replicates is even better!) Explain why you chose the datasets you did and how they will be used to answer your question. What particular features of that type of assay make it the best choice in order to answer your particular question? Make sure that for your second dataset, you can download processed data (a list of peaks, or DNA variants that were called).
-
Write up a proposal (half page, single spaced) explaining your question and computational approach. Feel free to use the literature to draw inspiration for your proposal (you will need to include literature citations in your final report).