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Series GSE66630 Query DataSets for GSE66630
Status Public on Dec 09, 2016
Title Transcriptome dynamics during the development of heart failure caused by mitochondrial complex I dysfunction and pressure overload
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Comprehensive knowledge of the dynamic changes in the cardiac transciptome can inform disease mechanism. Previous transcriptome profiling studies on heart failure rely on either microarray or RNA-Seq with low coverage, leaving a large portion of the transcriptome unexplored. Additionally, previous studies only examined two end stages of the disease, onset and late-stage heart failure. Profile of the transcriptome in the middle stage of disease progression can reveal critical molecular events underlying disease transition. Towards these goals, we conducted a multi-factorial RNA-Seq experiment, comparing the dynamic changes in the transcriptome of two murine models of heart failure, pressure overload and loss of mitochondrial complex I. Our data represents the deepest transcriptome coverage to date, covering onset, progression, and late stage of the disease. We found extensive differences in the expression magnitude and dynamics of the transciptomes in different heart failure models. In addition, such differences are associated with progressive worsening of cardiac physiology. Our analysis revealed that mitochondrial dysfunction combined with stress leads to increased number of differentially expressed long intergenic noncoding RNAs, including a recently identified lincRNA that is a master regulator of the cardiac lineage during development.
Overall design Cardiac tissues were cleaned with PBS and harvested at 1, 2, 4, and 8 weeks after surgeries by freezing in liquid nitrogen. Cardiac RNA profiles of wild type (WT) and ndufs4H-/- mice after surgeries were generated by deep sequencing at 4 time points, in quadruplicate, using Illumina HiSeq2000. The three factors of the data are genetic (WT vs. ndufs4H-/-), environmental stress (trans-aortic constriction vs. Sham controls), and time (Week 1, Week 2, Week 4 and Week 8). Thus, there are 16 samples in total and each sample has 4 replicates.
Contributor(s) Gao L, Lee CF, Ma X, Gao P, Gifford L, Karamanlidis G, Menendez L, Tian R, Tan K
Citation(s) 26083688
Submission date Mar 06, 2015
Last update date May 15, 2019
Contact name Long Gao
Phone 267-425-0053
Organization name The Children’s Hospital of Philadelphia
Lab Tan Lab
Street address 4002 Colket Translational Research Building (CTRB) 3501 Civic Center Boulevard
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (64)
GSM1626637 1W-WTSh1
GSM1626638 1W-WTSh2
GSM1626639 1W-WTSh3
BioProject PRJNA277489
SRA SRP055928

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Supplementary file Size Download File type/resource
GSE66630_HF_Ensembl_FPKM_All.xlsx.gz 15.2 Mb (ftp)(http) XLSX
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