DNA-PKcs RNASeq data: DNA-PKcs wilde-type or kinase-dead protein regulate basal and etoposide-induced gene expression changes

Maintenance of the genome is essential for cell survival, and impairment of the DNA damage response is associated with multiple pathologies including cancer and neurological abnormalities. DNA-PKcs is a DNA repair protein and a core component of the classical nonhomologous end-joining pathway, but it also has roles in modulating gene expression and thus, the overall cellular response to DNA damage. Using cells producing either wild-type (WT) or kinase-inactive (KR) DNA-PKcs, we assessed global alterations in gene expression in the absence or presence of DNA damage. We evaluated differential gene expression in untreated cells and observed differences in genes associated with cellular adhesion, cell cycle regulation, and inflammation-related pathways. Following exposure to etoposide, we compared how KR versus WT cells responded transcriptionally to DNA damage. Downregulated genes were mostly involved in protein, sugar, and nucleic acid biosynthesis pathways in both genotypes, but enriched..., The dataset contains ensemble ID, gene name if applicable, comparisons between genotypes with and without drug (etoposide) treatment. Within each comparison are log fold change, average expression, p value, and adjusted p value. 
Cells culture: V3-derived Chinese Hamster Ovary (CHO) cell lines were kindly provided by Dr. Katherine Meek, complemented with either human wild-type (WT), null (Null) or kinase inactivate DNA-PKcs, by K3753R mutation (KR), as previously reported (21). All cell lines were cultured in alpha-MEM (LifeTechnologies, Waltham, MA) supplemented with 10% FBS (MilliporeSigma, St. Louis, MO), 1% penicillin/streptomycin (LifeTechnologies), 200 µg/ml G418 (LifeTechnologies) and 10 µg/ml puromycin (Santa Cruz Biotechnology, Santa Cruz, CA) at 37ºC with 5% CO2and 100% humidity. All standard laboratory chemicals were purchased from MilliporeSigma unless otherwise indicated. Cells were cultured on 100 mm dishes overnight and next day, after washing, trizol reagent (MilliporeSi..., , This README File was generated 2024-02-28

## GENERAL INFORMATION

1. Title of Dataset: Comparative Analysis of Basal and
Etoposide-Induced Alterations in Gene Expression by DNA-PKcs Kinase Activity

2. Materials & Methods

a) Cell culture: V3-derived Chinese Hamster Ovary (CHO) cell lines were kindly provided by Dr. Katherine Meek, complemented with either human wild-type (WT), null (Null) or kinase inactivate DNA-PKcs, by K3753R mutation (KR), as previously reported (21) and designated as WT, Null and KR respectively in this study. All cell lines were cultured in alpha-MEM (LifeTechnologies, Waltham, MA) supplemented with 10% FBS (MilliporeSigma, St. Louis, MO), 1% penicillin/streptomycin (LifeTechnologies), 200 µg/ml G418 (LifeTechnologies) and 10 µg/ml puromycin (Santa Cruz Biotechnology, Santa Cruz, CA) at 37ºC with 5% CO2 and 100% humidity. All standard laboratory chemicals were purchased from MilliporeSigma unless otherwise indicated. Cells were cultured on 100 mm dishe...