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| Status |
Public on Nov 24, 2020 |
| Title |
Influence of histone lysine demethylase JMJD2-specific inhibition on the senescence-associated secretory phenotype developed in human stromal cells upon DNA damage |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Recent advances in next generation sequencing (NGS) has revolutionized system-based analysis of genome-wide expression, cellular pathways and responses. We performed this epigenetic study to streamline the transcriptome profiling (RNA-seq) of human stromal cells developing a typical senescence-associated secretory phenotype (SASP) upon stress induced by DNA damage or DNA damage together with pharmacological targeting of JMJD2, a trimethylation-specific demethylase of histone H3K9 and H3K36.
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| Overall design |
Overall transcript profiles of human primary prostate stromal cells (PSC27) were generated by deep sequencing in triplicate, using Illumina NovaSeq 6000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays
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| Contributor(s) |
Sun Y, Zhang B |
| Citation(s) |
32366480, 34263179 |
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Boyi Zhang, Qilai Long, Shanshan Wu, Qixia Xu, Shuling Song, Liu Han, Min Qian, Xiaohui Ren, Hanxin Liu, Jing Jiang, Jianming Guo, Xiaoling Zhang, Xing Chang, Qiang Fu, Eric W-F Lam, Judith Campisi, James L Kirkland and Yu Sun. KDM4 orchestrates epigenomic remodeling of senescent cells and potentiates the senescence-associated secretory phenotype. Nat Aging 1, 454-472 (2021). doi:10.1038/s43587-021-00063-1
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| Submission date |
Mar 14, 2019 |
| Last update date |
Jul 20, 2021 |
| Contact name |
Yu Sun |
| E-mail(s) |
sunyu@sinh.ac.cn, submarinesuny@yahoo.com
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| Phone |
86-21-54923302
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| Organization name |
Chinese Academy of Sciences
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| Department |
Shanghai Institute of Nutrition and Health
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| Lab |
Cancer Resistance
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| Street address |
320 Yueyang Rd, Life Sciences Building A #1508
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| City |
Shanghai |
| ZIP/Postal code |
200031 |
| Country |
China |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (9)
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| Relations |
| BioProject |
PRJNA527008 |
| SRA |
SRP188405 |
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