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@EugOT did we understand correctly? We have to select the gene(s) that determine the cell type? Or is it - determine single-cells that determine cell-type specific genes?

Process data set in 4 groups for further statistical analysis
-> 4 groups and their gene expression

Wich cell type do we want to focus on? -> find in paper
Which marker do we need for the cell type?

Our data is right skewed (a lot of zero values)
-> solve: Log10 transformation of data = reduce skewness of the AV

• dealing with zeros: add constant of 1 to every value of the AV (https://ubco-biology.github.io/BIOL202/transform.html)
• log transform all data

Analysis of data:
-> two factor ANOVA without measurement repetition

• prerequisites: Levene test -> is significant but because of the large amount of data it is acceptable to still do the ANOVA
• ANOVA: first look at the "Tests der Zwischensubjekteffekte": main effect sex; main effect condition; interaction effect -> which one is significant?
• ONLY if effect is significant, look at the "Paarweise Vergleiche" to find out which comparison in between the groups is significant

Find Syntax for SPSS and Output saved as file

What is a marker? Please save the paper you get the information from

After analysis of the data: Visualisation of results (see paper for examples)

In the notebooks from Evgenii he showed in the beginning, there are "pitfalls" for every step (all in all 10 steps). Check these pitfalls and think about how we can avoid them

Based on the paper, what do we expect to find in the brain area and cell type we chose when comparing female to male depressive patients? Write hypotheses

Dear @alex-prock , @alexgrent , @AnjaRejc , @Louises99 , @Takshoe , @venhoffl98 ,

I hope this message finds you in good health and spirits.

As we strive to continuously improve the quality of our courses, your feedback is invaluable. I kindly request a few minutes of your time to evaluate my teaching and contribution to the courses BVO: Introduction to Neuroscience (840.011) and SE TS: Introduction to Neuroscience (840.012) from the past winter semester.

Your insights and evaluations are not only greatly appreciated but also instrumental in enhancing the educational experience for future students and for my professional development.

I would be grateful if you could complete the evaluations at your earliest convenience.

When providing your feedback, I kindly ask that you focus on the sessions you attended, as this will give us the most accurate and helpful information to work with.

Additionally, I would like to remind you that some aspects of the course logistics, such as room allocations, the functionality of electronic platforms, and automatically generated emails, fall outside our control. For any comments related to these administrative and technical matters, please direct your feedback to katharina.stowasser-bloch(at)meduniwien.ac.at or tamara.peneder(at)meduniwien.ac.at.

Your participation in these evaluations is voluntary and anonymous, and I assure you that all your responses will be treated with the utmost confidentiality.

Course evaluation "Introduction to Neuroscience" (Course No.: 23W-840011), 2023 W (lectures)

https://eval.meduniwien.ac.at/evasys/online.php?pswd=RCAFU

Course evaluation "Introduction to Neuroscience (23W-840012)" (Course No.: 23W-840012), 2023 W (seminars)

https://eval.meduniwien.ac.at/evasys/online.php?pswd=HRDGA

Thank you in advance for your time and thoughtful input. Your contribution is crucial to creating a more effective learning environment and fostering academic excellence.

Warm regards,
Evgenii Tretiakov, PhD

Check what the task of the brain area is, the cells where coming from

What are the limitations mentioned in the paper (in the end)? Do they provide insight on how we could manage to avoid these?

What is single cell RNA sequencing? How would the work flow look?

2factor ANOVA without measure repeating
https://datatab.de/tutorial/zweifaktorielle-varianzanalyse-ohne-messwiederholung

factors:

1. sex
2. disorder

dependend variable: difference in gene-expression

pre-test:
normal distribution
homogeneity --> Levene test

How was the data prepared/cleaned in the paper? Which steps did they do before analyzing the data?

Nicely explained here: https://neuro.psychiatryonline.org/doi/10.1176/appi.neuropsych.21050136