KTH course: Applied Gene Technology and large-scale data analysis part-2

2. Papers and discussion

The 2nd aspect of the course is based on self learning. The techniques we learned can be divided into 4 main sub-fields:

  1. Hybridization technologies for genotyping and sequencing
  2. Long-read sequencing applied in epigenetics and haplotyping
  3. Single-cell strategies for transcriptomics, proteomics and open chromatin
  4. Spatially resolved transcriptomics by in situ and high-throughput sequencing

Post lectures, we had few lectures for discussing the gist of the papers from each sub-field and connecting them to the application of basic molecular tools that we learned throughout the lectures.

3. Projects

We formed groups of 4 students and selected sub-field of our interest. Each sub-field was selected by 2 groups. The aim of the project was to understand the papers in depth and present them to the class. The papers part of each sub-field were the proof of concept papers for various advanced technologies. For example, my group selected the 4th sub-field that had papers on spatial transcriptomics, in-situ sequencing and MER-FISH.

Spatial Transcriptomics workflow
Source:https://spatialtranscriptomics.com/

The best part of the project was the discussions, these discussions were not just among the group members but between groups. First the groups with same sub-field met to discuss doubts about the paper. This helped us understand and explain concepts thoroughly. Then in the next round of discussions, we read papers from all, the other groups and discussed it within the group as well as with the faculty. We also prepared a set of questions for each project.

My classmate Amparo presenting Barcoded Linked read sequencing technology

Finally, we presented the papers to fellow classmates by discussing the pros and cons of each method, its appropriate applications based on the information gathered and the technical and financial considerations of using the technique. This was followed by the question answer session, where the presenting group was questioned about the technique based on the pre-prepared questions.

The repetitive nature of the course helped understand and discuss various aspects of each technology. Further, the discussions enabled us to question the findings of a research paper as well as the technical details of any new technology in depth.

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