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Genome-wide Open Chromatin and Nucleosome Identification for ATAC-seq

Zhu, Jiaping (2023) Genome-wide Open Chromatin and Nucleosome Identification for ATAC-seq. Master's Thesis, University of Pittsburgh. (Unpublished)

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Abstract

Eukaryotic genomes are hierarchically packaged into chromatin, with open chromatin and nucleosome occupancy playing a crucial role in gene regulation. Understanding the intricate structure of chromatin is of utmost importance in epidemiology. The emergence of ATAC-seq is revolutionary, as it allows for the identification of both open chromatin and nucleosome on the same data set. A significant challenge in ATAC-seq lies in detecting and distinguishing regions from open chromatin and nucleosome. We introduce a novel method, ATACR, which capitalizes on two key features of ATAC-seq experiments: the preference of transposase Tn5 cutting at open chromatin regions and the distinctive pattern of fragment length distribution. Through implementation on Saccharomyces cerevisiae data sets, ATACR shows remarkable performance in accurately identifying open chromatin and nucleosome regions, surpassing other existing computational methods. It achieves higher detection accuracy within a broader range, making it a valuable tool for researchers in exploring chromatin organization and its impact on gene regulation.

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Details

Item Type: University of Pittsburgh ETD
Status: Unpublished
Creators/Authors:
CreatorsEmailPitt UsernameORCID
Zhu, Jiapingjiapingzhu@pitt.edujiz261
ETD Committee:
TitleMemberEmail AddressPitt UsernameORCID
Committee ChairHuang, Hengheng.huang@pitt.edu
Committee MemberZhan, Liangliang.zhan@pitt.edu
Committee MemberMao, Zhi-Hongzhm4@pitt.edu
Date: 14 September 2023
Date Type: Publication
Defense Date: 31 July 2023
Approval Date: 14 September 2023
Submission Date: 31 July 2023
Access Restriction: 1 year -- Restrict access to University of Pittsburgh for a period of 1 year.
Number of Pages: 37
Institution: University of Pittsburgh
Schools and Programs: Swanson School of Engineering > Electrical and Computer Engineering
Degree: MS - Master of Science
Thesis Type: Master's Thesis
Refereed: Yes
Uncontrolled Keywords: Open Chromatin, Nucleosome, ATAC-seq
Date Deposited: 14 Sep 2023 13:45
Last Modified: 14 Sep 2023 13:45
URI: http://d-scholarship.pitt.edu/id/eprint/45194

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