Projects
Name
Comparison of tissue specific gene regulation between dogs and humans
University
Sweden (IFMSA-Sweden) - Karolinska Institutet, Stockholm
Domain
Biology
Departement
Department of Biosciences and Nutrition
Head
Karl Ekwall
Tutor
Dr. Carsten Daub, Matthias Hörtenhuber, Abdul Kadir Mukarram
Languages
English (required)
Duration
4 weeks
Availability
Cities/Months Jan Feb Mar Apr May Jun Jul Augt Sep Oct Nov Dec
No No No No No Yes Yes Yes No No No No
Type of Research Project
- Basic science
What is the background of the project?
Model organisms are widely used in genetic research to facilitate discovery of various biological phenomena, including mechanisms of human diseases. Canis familiaris, commonly known as dog, is an important model for many diseases, including cancers, diabetes, and neuropsychiatric disorders. Beside sharing a high degree of morphological and genetic similarities with human, dogs also get similar human diseases with the same genetic factors. This makes it suitable to examine gene expression in dogs in relation human diseases.
What is the aim of the project?
We aim to strengthen dogs as a model organism for human health, by showing similarities between gene regulation in dogs and humans.
What techniques and methods are used?
We collected samples from several dog breeds and different tissues. We sequenced these samples using the Cap Analysis of Gene Expression-sequence (CAGE-seq) technique. The student will bioinformatically analyze these data of pathological and non-pathological tissues and compare them with publicly available human data sets. This analysis will be mainly done in R (which is a programmin language for statistical computing), using different packages.
What is the role of the student?
- The tasks of the student will be performed on his/her own
- The tasks will be done under supervision
What are the tasks expected to be accomplished by the student?
The student will analyze RNA CAGE-seq data with bioinformatics methods to a) identify tissue specific CAGE tag cluster (using the lab internal pipeline) b) identify tissue specific CAGE enhancers (using the lab internal pipeline) c) compare them to publicly available human enhancer data sets d) find coexpressed genes e) summarize the methods and results in a written report at the end of the internship (encouraged but not necessary)
Will there be any theoretical teaching provided (preliminary readings, lectures, courses, seminars etc)
Yes. The student will be asked to prepare via online tutorials about R and basic Linux commands provided by us.
What is expected from the student at the end of the research exchange? What will be the general outcome of the student?
- No specific outcome is expected
What skills are required of the student? Is there any special knowledge or a certain level of studies needed?
Interest in computational methods is required. Previous experiences with programming, especially R, are a plus.
Are there any legal limitations in the student’s involvement
No
Hours
8
Type of students accepted
This project accepts:
- Medical students
- Graduated students (less than 6 months)
- Pre-Medical students from the American-British system
- Students in biomedical fields
Articles
- Doggenomeannotation.Carsten O. Daub. 2019-04-04. https://www.doggenomeannotation.org/
- A promoter-level mammalian expression atlas. Nature volume 507; pages 462–470 (27 March 2014). doi: 10.1038/nature13182. https://www.nature.com/articles/nature13182