🕰 Time Estimation: 5 minutes
💬 Learning Objectives:
- Explain the experiment and its objectives.
We will be using the sequencing reads from the RNA-Seq dataset that is part of a larger study described in Kenny PJ et al, Cell Rep 2014.
RNA sequencing was performed on HEK293F cells which were either transfected with a MOV10 transgene, or siRNA to knock down Mov10 expression, or non-specific (irrelevant) siRNA. This resulted in 3 conditions Mov10 oe (over expression), Mov10 kd (knock down) and Irrelevant kd, respectively. The number of replicates is shown below.
Using these data, we will evaluate transcriptional patterns associated with perturbation of MOV10 expression. Please note that the irrelevant siRNA will be treated as our control condition.
What is the purpose of these datasets? What does Mov10 do?¶
The authors are investigating interactions between various genes involved in Fragile X syndrome, a disease in which there is aberrant production of the FMRP protein.
FMRP is “most commonly found in the brain, is essential for normal cognitive development and female reproductive function. Mutations of this gene can lead to fragile X syndrome, mental retardation, premature ovarian failure, autism, Parkinson's disease, developmental delays and other cognitive deficits.” - from Wikipedia
MOV10, is a putative RNA helicase that is also associated with FMRP in the context of the microRNA pathway.
The hypothesis the paper is testing is that FMRP and MOV10 associate and regulate the translation of a subset of RNAs.
- What patterns of expression can we identify with the loss or gain of MOV10?
- Are there any genes shared between the two conditions?
This lesson was originally developed by members of the teaching team (Mary Piper, Meeta Mistry, Radhika Khetani) at the Harvard Chan Bioinformatics Core (HBC).
Created: July 12, 2023