© 2024 Janghyun Choi
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.

Sequencing Techniques Portfolio

This portfolio showcases a variety of approaches to sequencing technology, focusing on the data processing and analysis of different samples. The purpose of this repository is not to present a single tool, but to display the range of techniques and coding strategies I have employed in my research. Each directory or section of this repository corresponds to different sequencing projects, including but not limited to RNA-seq and ChIP-seq analyses. These projects demonstrate how I handle diverse data sets and apply unique analysis methodologies. This portfolio is broadly organized into two main categories: data processing and data analysis (RNA/ChIP-seq).

Table of Contents

Data Processing

• Basal QC with FastQC
• Trimmed reads with Trimmomatic
• Mapping reads with HISAT2 for RNA-seq
• Mapping reads with Bowtie2 for ChIP-seq
• File Conversion and Management with SAMtools
• Feature counts with htseqCount
• File storage with Genozip
• Basal setting and troubleshooting

Data Analysis - RNA-seq

• Normalization and DEG analysis with edgeR
• DEG: Correlation plot
• DEG: Visualization - Volcano plot and Scatter plot
• DEG: Gene ontology and KEGG pathway analysis
• DEG: Heatmap

Data Analysis - ChIP-seq

• Exploring Sequencing Data with deepTools
• Efficient Analysis and Visualization of ChIP-seq Data with ngs.plot
• Peak detection: MACS3
• Peak detection: SICER2
• Peak Annotation with ChIPseeker
• Motif analysis with HOMER and MEME

Featured Projects

Project 1: Identification of Gene Expression and Chromatin Dynamics Changes During Oxidative Stress

• Description: In this project, we explored the effects of hydrogen peroxide-induced oxidative stress in a normal human keratinocyte cell line and three knockdown cell lines. We identified crucial changes in gene expression and chromatin dynamics of H3K4/H3K27me3, shedding light on the cellular mechanisms that activate NRF2-defense programs under oxidative stress.
• Techniques Used: RNA-seq and ChIP-seq
• Key Finding: Choi J & Lee H. Free Radic. Biol. Med. 217 (2024): 48-59. Pubmed
• Dataset: Access the detailed datasets from GEO SuperSeries GSE250128, including SubSeries GSE250126 and GSE250127.

Project 2: Establishing the Chromatin Landscape Regulating Stemness in Mesenchymal Stem Cells

• Description: We examined gene expression and chromatin alterations in normal and knockdown mesenchymal stem cell (MSC) lines exposed to differentiation stimuli. Our advanced bioinformatics analysis showed the critical roles of lineage-specific transcription factors and histone-modifying enzymes in maintaining MSC stemness and identity.
• Techniques Used: RNA-seq and ChIP-seq
• Key Findings: Choi J & Lee H. J. Biol. Chem. 299.10 (2023). Pubmed, Choi J & Lee H. Sci. Rep. 10.1 (2020): 3050. Pubmed
• Datasets: Further explore our findings with GEO SuperSeries GSE227538 and GSE131369.

Project 3: Comparative Transcriptome Analysis in Young vs. Middle-Aged Zebrafish Brains

• Description: We compared whole brain transcriptomes from 3-month-old and 12-month-old zebrafish to identify significant gene expression changes related to aging.
• Techniques Used: RNA-seq
• Status: The research findings are currently being prepared for submission. Upon acceptance of the paper, the dataset will be released to the public.

Project 4: Robust Link Between Gene Expression and Histone Dynamics During Short-Day Treatment in Plants

• Description: We studied gene expression and histone acetylation in normal and knockout plants under short-day (SD) treatment to reveal the epigenetic mechanisms that trigger flowering.
• Techniques Used: RNA-seq and ChIP-seq
• Status: The research findings are currently being prepared for submission. Upon acceptance of the paper, the dataset will be released to the public.

Implications of This Portfolio

This portfolio not only showcases a range of sophisticated sequencing techniques but also serves as a testament to my commitment to rigorous data analysis and innovative problem-solving in the field of genomics. The methodologies and strategies demonstrated here reflect my ability to adapt and optimize processes to meet the challenges presented by diverse datasets.

For newcomers to sequencing, this portfolio will act as a valuable learning resource. It offers practical examples and workflows that clarify RNA-seq and ChIP-seq analysis complexities. Sharing these insights allows me to support the broader community and help others master the latest sequencing technologies.

Furthermore, my work highlights the importance of transparency and reproducibility in scientific research. Each project within this repository is documented in a way that not only facilitates understanding but also enables others to replicate the results, fostering a culture of open science.

In conclusion, through this portfolio, I aim to demonstrate not just the technical skills necessary for high-quality genomic analysis but also my enthusiasm for advancing the field and educating others. I believe that the tools and techniques provided here will be invaluable for anyone looking to deepen their understanding of sequencing and its applications in modern biology.