Practice test Flashcards
A MLPA probe is composed of several sequences. Which sequences are universal for all probes in a MLPA assay?
The primer sequences
Which method identifies the expression patterns of genes AND fusion genes in patient cells?
RNA sequencing
What is the correct order of steps in the process of sequencing by synthesis, such as illumina sequencing?
Addition of dNTP’s, incorporation, camera detection, block removal
What type of error is introduced in the case of Multiple Comparison Problem analysis?
Type I error
In the lab, you have 6 human cell lines of different stages of colon-cancer. To investigate the development, you will perform a MicroArray experiment to determine which genes are involved in the development of this kind of cancer.
A) Which samples do you use in this microarray experiment and in what form do you incubate these samples on the microarray chip?
B) Which probes do you use in this microarray experiment and what do these probes represent?
C) Which array will you be using?
D) Explain how you could make technical and biological replicates for this experiment
A) mRN of the different cell lines, converted into cDNA and label with fluorescent labeled nucleotides
B) cDNA array: cDNA probes of all human genes
C) cDNA array because you would like to study all genes expressed
D) Biological: isolation from multiple cells in same developing stage
Technical: Multiple arrays, multiple RNA isolations
Explain the terms Co-expression and Co-regulation
Co-expression: about genes with a comparable expression profile over multiple experiments
Co-regulation: about genes with a regulation by a common TF or that act together in a cellular pathway
In a Mass Spectrum of a peptide, you observe a peak at 915,62 m/z. Considering that the distance between different isotope peaks is 1/3 m/z and knowing that in this case charges are caused by protons, what is the actual mass of the peptide
1/3 distance= 1/1/3= 3 charges.
m/z=m devided by z so m= m/z * z: 915,62 * 3= 2746,86. This still includes the 3 protons: 2746,86-3= 2743,86 Da
Which ionization technique is the most suited to identify proteins using MS?
ESI or MALDI since they are relatively soft ionization methods, leaving peptides intact
Metabolomics experiments are mostly performed using GC-MS (gas). However, not all metabolomics samples are directly suitable for analysis in the GC. Explain why and which possibilities you have to resolve this problem
Analysis by GC requires Volatile (stofjes moeten vluchtig zijn) compounds. Sometimes, metabolites are not volatile and can therefore not be analysed by GC-MS. A possibility to resolve this is to derivatize the metabolite (ex. methylation) to make it volatile and thus suitable for GC
