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Series GSE52314 Query DataSets for GSE52314
Status Public on Dec 01, 2013
Title Epigenetic regulation of the MEG3-DLK1 microRNA cluster in human Type 2 diabetic islets
Organism Homo sapiens
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary Type 2 diabetes mellitus (T2DM) is a multi-factorial disease characterized by the inability of beta-cells in the endocrine pancreas to produce sufficient amounts of insulin to overcome insulin resistance in peripheral tissue. To investigate the function of miRNAs in T2DM, we sequenced the small RNAs of human islets cells from diabetic and non-diabetic organ donors and identified a cluster of miRNAs in an imprinted locus on human chromosome 14 to be dramatically down-regulated in T2DM islets. These miRNAs are highly and specifically expressed in human beta-cells. The down-regulation of this imprinted locus strongly correlates with increased methylation of its promoter in T2DM islets, providing evidence for an epigenetic modification that contributes to the pathogenesis of T2DM. Targets of the Chr 14q32 cluster of miRNAs were identified by high-throughput sequencing of cross-linked and immunoprecipitated RNA (HITS-CLIP) of Argonaute. We have also identified a unique class of sequences, termed chimeric reads, that represent an in vivo ligation of miRNAs and their targets while in complex with Argonaute, and which allow for the direct identification of miRNA:target relationships in vivo.
Overall design There are three experiments in this submission. All are in human islets or islet cell types. The first is a comparison of miRNA levels in sorted alpha versus beta cells. There is one replicate for this experiment. The second experiment is to measure the expression of miRNAs in whole islets as a function of glucose levels. There are three levels and one replicate for each condition. The third exeriment is a comparison of whole islets taken from human donors that were suspected/confirmed Type 2 diabetic or considered controls. There are 3 controls and 4 T2D samples.
Contributor(s) Kameswaran1 V, Bramswig NC, McKenna LB, Penn M, Schug J, Chen Y, Won K, Choi I, Vourekas A, Hand NJ, Liu C, Naji A, Friedman JR, Kaestner KH
Citation(s) 24374217
Submission date Nov 12, 2013
Last update date May 15, 2019
Contact name Jonathan Schug
Phone 215 898 0773
Organization name University of Pennsylvania
Department School of Medicine
Lab Next-Generation Sequencing Core
Street address 12-156 Smilow Ctr Trans Research
City Philadelphia
State/province Pennsylvania
ZIP/Postal code 19104-5160
Country USA
Platforms (2)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (12)
GSM1262770 cell.alpha
GSM1262771 cell.beta
GSM1262772 Islet glucose-1
BioProject PRJNA227380
SRA SRP032953

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE52314_alpha_beta_counts.txt.gz 17.6 Kb (ftp)(http) TXT
GSE52314_islet_glucose_counts.txt.gz 55.8 Kb (ftp)(http) TXT
GSE52314_t2d-v-ctl-summary.txt.gz 31.0 Kb (ftp)(http) TXT
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