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Series GSE114722 Query DataSets for GSE114722
Status Public on Mar 20, 2019
Title Identification of coordinately regulated microRNA-gene networks that differ in baboons discordant for LDL-Cholesterol
Organism Papio hamadryas
Experiment type Expression profiling by high throughput sequencing
Summary Although the mechanisms underlying development of atherosclerosis are not well understood, LDL-C is known to influence expression of endothelial microRNAs (miRNAs) and gene-targets of miRNAs to promote cell senescence. However, the impact of LDL-C on expression of PBMC miRNAs and miRNA targeted genes in response to an atherogenic diet is not known. We hypothesized that miRNA expression profiles differ between baboons with low and high serum low-density lipoprotein cholesterol (LDL-C) concentrations in response to diet, and that microRNA-gene networks in baboons discordant for LDL-Cholesterol
We generated small RNA libraries from baboons differing in their LDL-C response to dietary fat and cholesterol (low LDL-C, n = 3; high LDL-C, n = 3) using liver biopsies collected before and after a high-cholesterol, high-fat (HCHF) challenge diet. We sequenced the libraries using Next-Generation Illumina sequencing methods, analyzed the data using mirTools software and identified 517 baboon miRNAs: 490 homologous to human and 27 novel miRNAs. HCHF diet elicited expression of more miRNAs compared to baseline (chow) diet for both low and high LDL-C baboons. Seventeen miRNAs exhibited significant differential expression in response to HCHF diet in high LDL-C baboons compared to nine miRNAs in low LDL-C baboons. Putative miRNA targets were identified with TargetScan/Base tools. miRNAs significantly targeted more genes in high LDL-C baboons compared to low LDL-C responders. Further, we identified miRNA isomers and other non-coding RNAs that were differentially expressed in response to the challenge diet.Our discovery of differentially expressed baboon miRNAs and their targets is a fundamental step in understanding the role of non-coding RNAs in the modulation of dsylipidemia.
 
Overall design Assess the differential miRNAs and genes response to a high-cholesterol, high-fat diet in blood of low and high LDL-C baboons, and identify potential miRNA targets and corodinated network.
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This represents the mRNA component only
 
Contributor(s) Karere GM, Glenn JP, Birnbaum S, Garcia R, VandeBerg JL, Cox LA
Citation(s) 30875406
Submission date May 21, 2018
Last update date Mar 20, 2019
Contact name Genesio Karere
E-mail(s) gkarere@wakehealth.edu
Organization name Wake Forest Baptist Health Sciences
Department Internal Medicne
Street address 1 medical center blvd
City Winston-Salem
State/province NC
ZIP/Postal code 78227
Country USA
 
Platforms (1)
GPL25014 Illumina HiSeq 2500 (Papio hamadryas)
Samples (12)
GSM3148553 Sample_Baboon_1x3817_highLDL_chow_RNA_seq_31
GSM3148554 Sample_Baboon_1x3817_highLDL_HCHF_RNA_seq_32
GSM3148555 Sample_Baboon_1x4154_highLDL_chow_RNA_seq_37
Relations
BioProject PRJNA472374
SRA SRP148590

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE114722_processed_raw_data_gmkarere.xlsx 3.0 Mb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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