RNA-seq and label-free quantitative proteomics data from: KDM4A serves as an α-tubulin demethylase regulating microtubule polymerization and cell mitosis
Data files
Sep 19, 2025 version files 37.38 GB
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Proteomics-dTAG-0_h-rep1.raw
1.45 GB
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Proteomics-dTAG-0_h-rep2.raw
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Proteomics-dTAG-0_h-rep3.raw
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Proteomics-dTAG-12_h-rep1.raw
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Proteomics-dTAG-12_h-rep2.raw
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Proteomics-dTAG-12_h-rep3.raw
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README.md
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RNA-dTAG-0_h-rep1_1.fq.gz
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RNA-dTAG-0_h-rep1_2.fq.gz
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RNA-dTAG-0_h-rep2_1.fq.gz
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RNA-dTAG-0_h-rep2_2.fq.gz
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RNA-dTAG-0_h-rep3_1.fq.gz
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RNA-dTAG-0_h-rep3_2.fq.gz
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RNA-dTAG-12_h-rep1_1.fq.gz
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RNA-dTAG-12_h-rep1_2.fq.gz
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RNA-dTAG-12_h-rep2_1.fq.gz
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RNA-dTAG-12_h-rep2_2.fq.gz
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RNA-dTAG-12_h-rep3_1.fq.gz
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RNA-dTAG-12_h-rep3_2.fq.gz
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Abstract
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.
Dataset DOI: [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-FKBP12F36V-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.