Mugisha, Samson; Labhsetwar, Shreyas; Dave, Devam; Klemke, Richard; Desgrosellier, Jay S. (2025). A dataset of chronic nicotine-induced genes in HCC38 breast cancer cells. UC San Diego Library Digital Collections. https://doi.org/10.6075/J04X585F

PyDESeq2 and Velocyto (0.6) were used to generate differentially expressed genes (DEG) and identify the most dynamic genes in chronic nicotine-treated and control cells.

• 2024

• 2025

• Mugisha, Samson

• Desgrosellier, Jay S.

• Dave, Devam
• Klemke, Richard
• Labhsetwar, Shreyas

For differential gene expression analysis, PyDESeq2 was used to estimate variance-mean dependence in count data from sequencing assays and test for differential expression based on a model using the negative binomial distribution. Velocyto (0.6) was used to estimate the spliced and unspliced counts from the pre-aligned bam files for the dynamic trajectory analysis.

This research was supported by funding from a Tobacco-Related Disease Research Program (TRDRP) High Impact Research Project Award 28IR-0054 (to J.S.D.) and a California Breast Cancer Research Program Grant B28IB5479 (to J.S.D.).

• Biochemistry and cell biology
• Biological sciences
• Breast cancer
• Gene expression
• Human Breast Cancer Cell Line: HCC38
• Inflammation
• Nicotine
• Single-cell RNA-seq
• Smoking
• Tobacco products

• data

• English

Identifier: Samson Mugisha: https://orcid.org/0000-0003-1528-204X

Primary associated publication

• Mugisha, S., Baba, S.A., Labhsetwar, S. et al. S100A8/A9 innate immune signaling as a distinct mechanism driving progression of smoking-related breast cancers. Oncogene (2025). https://doi.org/10.1038/s41388-025-03276-5

Software

• 10x Genomics Single Cell Analysis (on GitHub): https://github.com/10XGenomics/cellranger
• DESeq2: http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html
• Implementation of the Leiden algorithm for various quality functions to be used with igraph in Python (on GitHib): https://github.com/vtraag/leidenalg
• velocyto (velocyto.org)

Other version

• RNA sequencing data that support the findings of this study have been deposited in the NCBI Sequence Read Archive (SRA) with the primary accession code PRJNA1145480. scRNA-seq of HCC38 Nicotine (nicotine-treated group): https://www.ncbi.nlm.nih.gov/sra/SRX25630994
• RNA sequencing data that support the findings of this study have been deposited in the NCBI Sequence Read Archive (SRA) with the primary accession code PRJNA1145480. scRNA-seq of HCC38 Vehicle (control group): https://www.ncbi.nlm.nih.gov/sra/SRX25630993

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2025-03-04