DOI: 10.5061/dryad.63xsj3vdg
title: RNA-seq and label-free quantitative proteomics data from: KDM4A serves as an α-tubulin demethylase regulating microtubule polymerization and cell mitosis

description: Tri-methylation on lysine 40 of α-tubulin is involved in cell division and
 neuronal development. We report that KDM4A, a member of the histone
 demethylase family, demethylates α-tubulin. Degradation of KDM4A for 12 h
 leads to an increase in methylation of α-tubulin and histone, as well as
 mitotic defects in KDM4A-FKBP12F36V-2×HA-T2A-Puro knock-in HEK293T cells
 (termed as KDM4A-dTAG cells). We performed RNA-seq and label-free
 quantitative proteomics to evaluate the consequence of genetic alteration
 resulting from an increase in histone methylation in KDM4A-dTAG cells upon
 12 h of dTAG-13 treatment. Notably, we identified 23 genes that
 showed more than 1.5-fold expression change after 12 h of dTAG-13
 treatment, with 13 up-regulated and 10 down-regulated genes,
 and 16 proteins showed more than 1.5-fold expression alteration
 except KDM4A, including 10 up-regulated and 6 down-regulated
 proteins. This dataset contains all raw data of RNA-seq
 and label-free quantitative proteomics described in this study.
description: # RNA-seq and label-free quantitative proteomics data from: KDM4A serves
 as an α-tubulin demethylase regulating microtubule polymerization and cell
 mitosis Dataset DOI: [[10.5061/dryad.63xsj3vdg\]
 ](10.5061/dryad.63xsj3vdg) ## Description of the data and file structure
 This dataset is associated with Cao et al. 2025. KDM4A serves as an
 α-tubulin demethylase regulating microtubule polymerization and cell
 mitosis In this study, We performed RNA-seq and label-free quantitative
 proteomics to evaluate the consequence of genetic alteration resulting
 from an increase of histone methylation in
 KDM4A-FKBP12^F36V^-2×HA-T2A-Puro knock-in HEK293T cells (termed as
 KDM4A-dTAG cells) upon 12 h of dTAG-13 treatment. Total RNA was isolated
 from KDM4A-dTAG cells treated with 100 nM dTAG-13 for 0 or 12 h using
 RNeasy mini kit (Qiagen, Germany) and sequenced on the Illumina HiSeq
 X-ten (Illumina). Total protein was extracted from KDM4A-dTAG cells
 treated with 100 nM dTAG-13 for 0 or 12 h using RIPA buffer [50 mM
 Tris-HCl, PH 7.4, 150 mM NaCl,1% Triton X-100, 1 mM EDTA, 10% glycerol and
 1× cOmplete protease inhibitor cocktail (Roche)] and identified with an
 Orbitrap Eclipse Tribrid mass spectrometer (Thermo Scientific). All
 methods follow the manufactures recommendations. This dataset contains all
 raw data of RNA-seq and label-free quantitative proteomics described in
 this study. ### Files and variables * File: Proteomics-dTAG-0_h-rep1.raw
 Description: Raw label-free quantitative proteomics data for KDM4A-dTAG
 cells treated with 100 nM dTAG-13 for 0 h (first biological replicate). *
 File: Proteomics-dTAG-0_h-rep2.raw Description: Raw label-free
 quantitative proteomics data for KDM4A-dTAG cells treated with 100 nM
 dTAG-13 for 0 h (second biological replicate). *
 File: Proteomics-dTAG-0_h-rep3.raw Description: Raw label-free
 quantitative proteomics data for KDM4A-dTAG cells treated with 100 nM
 dTAG-13 for 0 h (third biological replicate). *
 File: Proteomics-dTAG-12_h-rep1.raw Description: Raw label-free
 quantitative proteomics data for KDM4A-dTAG cells treated with 100 nM
 dTAG-13 for 12 h (first biological replicate). *
 File: Proteomics-dTAG-12_h-rep2.raw Description: Raw label-free
 quantitative proteomics data for KDM4A-dTAG cells treated with 100 nM
 dTAG-13 for 12 h (second biological replicate). *
 File: Proteomics-dTAG-12_h-rep3.raw Description: Raw label-free
 quantitative proteomics data for KDM4A-dTAG cells treated with 100 nM
 dTAG-13 for 12 h (third biological replicate). * Files:
 RNA-dTAG-0_h-rep1_1.fq.gz and RNA-dTAG-0_h-rep1_2.fq.gz Description: Raw
 pair-end RNA-seq data for KDM4A-dTAG cells treated with 100 nM dTAG-13 for
 0 h (first biological replicate). * Files: RNA-dTAG-0_h-rep2_1.fq.gz
 and RNA-dTAG-0_h-rep2_2.fq.gz Description: Raw pair-end RNA-seq data
 for KDM4A-dTAG cells treated with 100 nM dTAG-13 for 0 h (second
 biological replicate). * Files: RNA-dTAG-0_h-rep3_1.fq.gz
 and RNA-dTAG-0_h-rep3_2.fq.gz Description: Raw pair-end RNA-seq data
 for KDM4A-dTAG cells treated with 100 nM dTAG-13 for 0 h (third biological
 replicate). * Files: RNA-dTAG-12_h-rep1_1.fq.gz
 and RNA-dTAG-12_h-rep1_2.fq.gz Description: Raw pair-end RNA-seq data
 for KDM4A-dTAG cells treated with 100 nM dTAG-13 for 12 h (first
 biological replicate). * Files: RNA-dTAG-12_h-rep2_1.fq.gz
 and RNA-dTAG-12_h-rep2_2.fq.gz Description: Raw pair-end RNA-seq data
 for KDM4A-dTAG cells treated with 100 nM dTAG-13 for 12 h (second
 biological replicate). * Files: RNA-dTAG-12_h-rep3_1.fq.gz
 and RNA-dTAG-12_h-rep3_2.fq.gz Description: Raw pair-end RNA-seq data
 for KDM4A-dTAG cells treated with 100 nM dTAG-13 for 12 h (third
 biological replicate). ## Code/software The RNA-seq data were sequenced on
 the Illumina HiSeq X-ten (Illumina) and analyzed with in R (version
 4.3.3), using the DESeq2 (version 1.42.1) package. The label-free
 quantitative proteomics data were obtained from Orbitrap Eclipse Tribrid
 mass spectrometer (Thermo Scientific) and analyzed with MaxQuant.