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Series GSE152146 Query DataSets for GSE152146
Status Public on Nov 12, 2020
Title TNF induced inflammatory transcription dynamics and epigenetic changes
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary TNF can induce inflammatory responses in cells, including transcriptional and epigenetic changes. To investigate the long-term influence of TNF stimulation on epigenetic modifications, we did transcriptomic and epigenomic profiling of TNF-treated cells with various time length or stages.
 
Overall design HEK 293 cells were treated with short-term (12 h) and long-term (12 d) TNF, withdrawn TNF to recover 10 d (12 d + 10 d), and treated with 12 h TNF again (12 d + 10 d + 12 h). p65 ChIP-seq and RNA-seq were done for those samples, in WT and TET gene KO cells respectively. WGBS experiments were also performed to obtain DNA methylation data for these samples. H3K27ac ChIP-seq were used to profile histone modifications at p65 binding sites. ATAC-seq experiments were performed to measure chromatin accessibility under various types of treatments.
 
Contributor(s) Zhao Z, Zhang Z, Li J, Dong Q, Xiong J, Li Y, Lan M, Zhu B
Citation(s) 33155547
Submission date Jun 09, 2020
Last update date Nov 15, 2020
Contact name Zhuqiang Zhang
E-mail(s) zhangzhuqiang@ibp.ac.cn
Organization name Institute of Biophysics, CAS
Street address 15 Datun Road, Chaoyang District.
City Beijing
State/province ---
ZIP/Postal code 100101
Country China
 
Platforms (2)
GPL23227 BGISEQ-500 (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (58)
GSM4604852 p65-TNF-12d+withdraw-10d
GSM4604853 p65-TNF-12d+withdraw-10d+TNF12h
GSM4715082 non-treated control RNA-seq, rep1
Relations
BioProject PRJNA638409
SRA SRP266653

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Supplementary file Size Download File type/resource
GSE152146_RAW.tar 5.2 Gb (http)(custom) TAR (of BIGWIG, COV, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
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