Undergrad Research Experience: Difference between revisions
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** [https://msphere.asm.org/content/3/2/e00089-18 Fletcher et al (2018).] | ** [https://msphere.asm.org/content/3/2/e00089-18 Fletcher et al (2018).] | ||
** [https://www.sciencedirect.com/science/article/pii/S0944501318301988?via%3Dihub Gu et al (2018)] | ** [https://www.sciencedirect.com/science/article/pii/S0944501318301988?via%3Dihub Gu et al (2018)] | ||
* Data set: on "genometracker.org" | * Data set: posted on "genometracker.org" | ||
** Wild type transcriptome at 12 hour, paired-end read files: | |||
** /home/azureuser/18134XR-29-01_S0_L001_R1_001.fastq.gz | |||
** /home/azureuser/18134XR-29-01_S0_L001_R2_001.fastq.gz | |||
* To Do | * To Do | ||
** 9/8/2020 12 noon: Demo on read quality using FastQC and mapping reads to reference genomes with bowtie | ** 9/8/2020 12 noon: Demo on read quality using FastQC and mapping reads to reference genomes with bowtie | ||
Revision as of 21:01, 1 September 2020
Fall 2020
Participants
- 'Eamen Ho': Volunteer research assistant
- 'Ramandeep Singh': BIOL 48002
- 'Desiree Pante': BIOL 48001
- 'Afsana Rahman': Volunteer research assistant
- 'Roman Shimonov': BIOL 48002
- 'Justin Hiraldo': BIOL 48002
- 'Zaheen Hossain': Volunteer research assistant
Schedule
- Tuesdays at 12 noon - 2pm by Zoom
- Sept 1, 2020. Week 1. Meet & Greet; Intro to projects
- Sept 8, 2020. Week 2. Presentations (background, data, and methods), based on assigned readings
Project 1. Structure & evolution of multipartite genome of Lyme disease bacteria
- Participants: Desiree & Ramon
- Readings
- Review: deCenzo & Finan (2017).
- Data set: lp54 & cp26 plasmids
- TO DO:
- 9/8/2020, 12 noon: 5-slides presentation on multipartite bacterial genome evolution (based on the paper above)
Project 2. OspC Cross-reactivity analysis
- Participants: Justin, Roman
- Readings: Ivanova et al (2009)
- Tool: ImageJ
- Data set (to be sent)
- To Do
- 9/8/2020 12 noon: 5-slide presentation on background, material & methods, and data capture using ImageJ
Project 3. Clostridium transcriptome analysis
- Participants: Eaman, Zaheen
- Readings
- Data set: posted on "genometracker.org"
- Wild type transcriptome at 12 hour, paired-end read files:
- /home/azureuser/18134XR-29-01_S0_L001_R1_001.fastq.gz
- /home/azureuser/18134XR-29-01_S0_L001_R2_001.fastq.gz
- To Do
- 9/8/2020 12 noon: Demo on read quality using FastQC and mapping reads to reference genomes with bowtie