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Series GSE51169 Query DataSets for GSE51169
Status Public on Feb 27, 2014
Title Dynamic Reorganization of the Cardiomyocyte Transcriptome in Response to TNFα-induced Proinflammatory Signaling [ChIP-Seq]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Inflammation is associated with many cardiovascular pathologies, but the underlying mechanisms remain unclear. To explore this in more detail, we characterized the transcriptome of an immortalized adult human ventricular cardiomyocyte cell line (AC16) in response to tumor necrosis factor (TNFa). Using a combination of genomic approaches, including global nuclear run-on sequencing (GRO-seq) and chromatin immunoprecipitation coupled with sequencing (ChIP-seq), we identified ~30,000 transcribed regions in AC16 cells, which includes a set of RNA polymerases I and III (Pol I and Pol III) transcribed regions revealed in the presence of α-amanitin. The set of transcribed regions produces both protein-coding and non-coding RNAs, many of which have not been annotated previously, including enhancer RNAs originating from NF-κB binding sites. In addition, we observed that AC16 cells rapidly and dynamically reorganize their transcriptomes in response to TNFa stimulation in an NF-κB-dependent manner, switching from a basal state to a proinflammatory state affecting a spectrum of cardiac-associated protein-coding and non-coding genes. Moreover, we observed distinct Pol II dynamics for up- and downregulated genes, with a rapid release of Pol II into productive elongation for TNFa-stimulated genes. Our studies shed new light on the regulation of the cardiomyocyte transcriptome in response to a proinflammatory signal and help to clarify the link between inflammation and cardiomyocyte function at the transcriptional level.
Overall design Using GRO-seq and ChIP-seq (p65 and RNA Pol II) over a time course of TNFα signaling in AC16 human cardiomyocytes.
Contributor(s) Luo X, Chae M, Krishnakumar R, Danko CG, Kraus WL
Citation(s) 24564208
Submission date Sep 25, 2013
Last update date May 15, 2019
Contact name W. Lee Kraus
Organization name UT Southwestern Medical Center
Street address 5323 Harry Hines Blvd.
City Dallas
State/province TX
ZIP/Postal code 75390-8511
Country USA
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (8)
GSM1239995 p65_ChIP-seq_Vehicle_1
GSM1239996 p65_ChIP-seq_Vehicle_2
GSM1239997 p65_ChIP-seq_TNFα_1
This SubSeries is part of SuperSeries:
GSE51225 Dynamic Reorganization of the Cardiomyocyte Transcriptome in Response to TNFα-induced Proinflammatory Signaling
BioProject PRJNA223647
SRA SRP031851

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Supplementary file Size Download File type/resource
GSE51169_RAW.tar 1.6 Gb (http)(custom) TAR (of BED, WIG)
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Raw data are available in SRA
Processed data provided as supplementary file

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