SUPR
Functional Genomics
Dnr:

NAISS 2023/23-414

Type:

NAISS Small Storage

Principal Investigator:

Debora Parrine

Affiliation:

Uppsala universitet

Start Date:

2023-08-23

End Date:

2024-09-01

Primary Classification:

10203: Bioinformatics (Computational Biology) (applications to be 10610)

Webpage:

Allocation

Abstract

Treatment of pancreatic cancer has been a challenge to the scientific world, partly due to the lack of knowledge on how the disease settles, and no effective treatment has been discovered so far. We want to study a new uncharacterized in the context of pancreatic cancer and answer the question of why it is a bad prognosis for pancreatic cancer. We believe that this knowledge will later help in developing methods for treatment, or diagnosis of pancreatic cancer and maybe other types of cancer. We previously found that this gene has an impact on chromatin modelling by changing the acetylation patterns in histones, especially histone 3. To better understand the chromatin accessibility impact of this gene, we generated pancreatic cancer knockout cell lines and performed ATAC-seq analysis. The results of this analysis will allow us to find the precise locations of the chromatin modifications and it will answer the main question: is this gene a repressor or activator of chromatin remodelling proteins? This proposal refers to NGS data to characterize the function of a new gene. In particular, we would like to run ATAC-seq analysis, using the NF-core/atacseq nextflow pipeline.