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KTH course: Applied Gene Technology and large-scale data analysis part-1

Welcome to the KTH semester! This course was the best course throughout the Masters.

The main aim of the course is to familiarize us to the advanced technologies in the field of transcriptomics while understanding the advantages and disadvantages of one over the other; thus, allowing us to make the decisions to use these advanced methods in the correct context of research questions. Further, it acclimatizes us to handle and perform basic analysis on various forms of RNA-seq datasets and make biological interpretations.

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The course is handled by 3 professors.

Patrik Ståhl, Stefania Giacomello, and Olof Emanuelsson. Patrik was the main course responsible and took most of the classes on different technologies. Stefania covered the topics related to single cell sequencing technologies and Olof introduced to the theory behind the large-scale data analysis and the practical aspects of the same.

The part of course taught by Patrik can be separated into 3 sections:

  1. Theory lectures
  2. Papers and discussions
  3. Projects


  1. Theory lectures

The theory lectures covered the various technologies right from molecular inversion probe, microarray, variations of bead array, various forms RNA FISH, conventional Sanger and Illumina sequencing to the various forms of advanced sequencing methods based on Illumina platform and last but not the least an introduction to the field of Spatial transcriptomics.

The lectures were mainly short introduction to the concepts behind these and other basic tools in molecular biology to enable us to understand the advanced technical details upcoming in the next section of the course i.e. from the original papers of these technologies.

This is mostly covered in the first 2 weeks of the course, and forms important base for the rest of the course. Since, I was doing my internship, I was not able to attend this part of the course, I have written based on the information from my classmates.

Advice: I strongly recommend to attend all classes right from the beginning and not be late when returning from summer vacation, it can get very difficult to cope up with many things that run in parallel.