Program Overview

Course Overview

The course CB207V, Computational Analyses of mRNA-seq, ChIP-seq and ATAC-seq, provides theoretical and practical knowledge in analyses of mRNA-seq, ChIP-seq, and ATAC-seq data. The course aims to characterize open chromatin regions, identify protein binding sites across the genome, and quantify mRNA expression in human cells.

Information per Course Offering

• Termin: Spring 2026
• Course Location: KTH Solna
• Duration: 13 Jan 2026 - 14 Mar 2026
• Periods: Spring 2026: P3 (7.5 hp)
• Pace of Study: 50%
• Application Code: 10310
• Form of Study: Distance Daytime
• Language of Instruction: English
• Number of Places: 5 - 60

Course Syllabus

The course syllabus is available in an accessible format on this page. Headings with content from the Course syllabus are denoted with an asterisk.

Content and Learning Outcomes

Course Disposition

Preliminary schedule and course information can be found on the course page.

Course Contents

• Introduction to Genomics - Genomics, epigenomics, and analyses of chromatin
• Introduction to Transcriptomics - Capturing the distinct RNAs in the cell
• The Genome Regulators - Readers, writers, insulators, TFs, Pols, helicases
• Biochemical Foundations - From molecular capture to libraries and reads
• Sequencing - Adapters, UMIs, clusters, sequencing-by-synthesis
• Mapping the Reads - From fastq to bigwigs and peak files
• Computational Foundations - Basics in shell scripting and R
• ChIP-seq and ATAC-seq Data - Protein-DNA interactions and accessible regions
• MEME-ChIP - DNA elements directing protein binding
• mRNA-seq - Quantifying gene expression and tracking changes in mRNA levels
• DESeq2 and Gene Ontology - Differential expression and transcriptional responses
• Integrating Genomic Datasets - Integrating and visualizing large-scale data
• Open Access for Data and Code - GEO, SRA, ENCODE, GitHub
• Systems on Systems - Epigenetic pattern recognition, identification of functional genomic regions
• Challenges and Future Directions - Normalization, resolution, purity, machine learning in genomics

Intended Learning Outcomes

After completion of the course, students shall have knowledge to:

• Describe genomics, epigenomics, and how distinct proteins and RNAs coordinate chromatin state and transcription
• Describe readers, writers, transcription factors, co-factors, general transcription factors, RNA Polymerases, DNA Polymerases, negative elongation factors, positive elongation factors, RNA binding proteins, and Topoisomerases
• Give characteristics of functional genomic regions, including enhancers, promoters, insulators, gene bodies, and termination windows
• Explain how histone modifications and chromatin compartments can influence chromatin accessibility, DNA repair, DNA synthesis, and transcription
• Obtain ChIP-seq, mRNA-seq, and ATAC-seq datasets from public repositories
• Understand the process of sequencing techniques from biochemistry to data analyses
• Map protein binding sites and open chromatin regions
• Quantify mRNA levels and perform differential gene expression analyses
• Perform gene ontology analyses and investigate transcriptional responses
• Understand the concept of large-scale data and how machine learning can be integrated into genomics

Literature and Preparations

Specific Prerequisites

Completed degree project with at least 15 credits, and 7.5 credits studies in cell biology, molecular biology, genomics, biotechnology, or bio(medical) sciences. English B/6.

Literature

Information about course literature can be found in the course memo for the course offering or in the course room in Canvas.

Examination and Completion

Grading Scale

P, F

Examination

• DEL1 - 80% presence and completed exercises, 4.0 credits, grading scale: P, F
• SEM1 - Group work and seminar presentation, 1.0 credits, grading scale: P, F
• PRO1 - Group project completed, 2.5 credits, grading scale: P, F

Examiner

Anniina Vihervaara

Ethical Approach

• All members of a group are responsible for the group's work
• In any assessment, every student shall honestly disclose any help received and sources used
• In an oral assessment, every student shall be able to present and answer questions about the entire assignment and solution

Further Information

Offered By

CBH/Gene Technology

Main Field of Study

Biotechnology

Education Cycle

Second cycle