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Introduction
Personal
Motivation
Bioinformatics
Statistics
Coding
Bursary
Summary
Biological study design and interpretation
This set of questions checks that you understand basics of biological study design and can critically interpret presented results.
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B1
You performed bulk transcriptomic sequencing of mouse blood samples. However, when you tried to align the reads to a reference genome, you found: 0% uniquely mapped reads, 10% multi-mapped reads, and 90% unmapped reads. Which of the following options cannot explain the failure in mapping:
Samples have been contaminated
Adapter trimming was not performed
You did not deplete the ribosomal RNA
You are aligning with the wrong reference genome
The sequencing quality was poor
B2
In
this
2013 paper, Christenson et al. investigated the role of miR-638 microRNA in Chronic Obstructive Pulmonary Disease (COPD). The figure below is an ECDF plot that shows the effect of miR-638 inhibition on COPD fibroblast gene expression. Based on the plot, which of the following statement(s) is/are correct?
On average, miR-638 targets are upregulated in the transfected COPD fibroblasts compared to the set of all genes
On average, miR-638 targets are downregulated in the transfected COPD macrophages compared to the set of all genes
On average, miR-638 targets are downregulated in the transfected COPD fibroblasts compared to the set of all genes
miR-638 activity downregulates target genes in COPD fibroblasts
miR-638 activity upregulates target genes in COPD fibroblasts
Figure for B2
B3
You are analyzing genomic data from an organism with an unknown reference. Which of the following genome assembly strategies would be the most appropriate in this case?
De novo assembly using high-quality short reads only
De novo assembly using long or ultra-long reads only
Hybrid de novo assembly using short and long reads
Alignment to a closely related reference genome
A metagenomics-like assembly approach (utilizing a database of genomes)
B4
Ziff et al., 2023
describes the transcriptional landscape of Amyotrophic Lateral Sclerosis (ALS), a disease that causes motor neuron loss and often involves TDP-43 protein abnormalities. The analysis involved transcriptomic profiling of in vitro motor neuron samples generated using induced pluripotent stem cells derived from ALS patients and non-ALS controls (CTRL). Based on the volcano plot below, which of the following statements is/are
false
?
TCEAL6 expression is higher in CTRL
CDKN1A is up-regulated in ALS compared to CTRL
The p-value for CHRND differential gene expression is lower than that of MYOG
The p-value cutoff for differentially expressed genes in this plot is 4
The p-value cutoff for differentially expressed genes in this plot is 1.3
Figure for B4
B5
To study the role of Dlx5 in mouse pup development, you used CRISPR-Cas9 technology to knock out that gene. CRISPR-Cas9 looked for a place in the genome that should be targeted, and Cas9 introduced a break. What are the primary DNA repair mechanisms the cell uses after CRISPR-Cas9’s activity, taking into account that it is a transcription factor that requires the 5'-TAATTA-3' consensus sequence for DNA binding?
base excision repair
mismatch repair
non-homologous recombination
microhomology-mediated end joining