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CB207V Computational Analyses of mRNA-seq, ChIP-seq and ATAC-seq 7.5 credits

The course provides theoretical and practical knowledge in analyses of mRNA-seq, ChIP-seq and ATAC-seq data. During the course, the participants characterise open chromatin regions, identify protein binding sites across the genome, and quantify mRNA expression in human cells.

Information per course offering

Termin

Information for Spring 2025 Start 14 Jan 2025 single courses students

Course location

KTH Solna

Duration
14 Jan 2025 - 16 Mar 2025
Periods
P3 (7.5 hp)
Pace of study

50%

Application code

20044

Form of study

Distance Daytime

Language of instruction

English

Course memo
Course memo is not published
Number of places

5 - 60

Target group
No information inserted
Planned modular schedule
[object Object]
Part of programme
No information inserted

Contact

Examiner
No information inserted
Course coordinator
No information inserted
Teachers
No information inserted

Course syllabus as PDF

Please note: all information from the Course syllabus is available on this page in an accessible format.

Course syllabus CB207V (Spring 2025–)
Headings with content from the Course syllabus CB207V (Spring 2025–) are denoted with an asterisk ( )

Content and learning outcomes

Course disposition

Preliminary schedule and course info can be found here: https://tinyurl.com/CB207V-2025

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. Functional analyses of DNA-binding proteins.
  • Challenges and future directions - Normalization, resolution, purity. Machine learning in genomics.

Intended learning outcomes

After completion of the course, the 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 dataanalyses.
  • 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

You can find information about course literature either in the course memo for the course offering or in the course room in Canvas.

Examination and completion

If the course is discontinued, students may request to be examined during the following two academic years.

Grading scale

P, F

Examination

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

Based on recommendation from KTH’s coordinator for disabilities, the examiner will decide how to adapt an examination for students with documented disability.

The examiner may apply another examination format when re-examining individual students.

Examiner

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

Course room in Canvas

Registered students find further information about the implementation of the course in the course room in Canvas. A link to the course room can be found under the tab Studies in the Personal menu at the start of the course.

Offered by

Main field of study

Biotechnology

Education cycle

Second cycle