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| Status |
Public on Aug 24, 2020 |
| Title |
Genome-Wide Profiling of DNA Methylation and Gene Expression Identifies Candidate Genes for Human Diabetic Neuropathy (RRBS) |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by high throughput sequencing
|
| Summary |
We perfomed transcriptomic and methylomic analysis of sural nerve biopsies from type 2 diabetic patients with neuropathy. Sural nerve transcriptomic and methylomic profiles were integrated and subsequent biological meaning investigated using KEGG pathway analysis of overlapping differentially expressed genes (DEGs) and differentially methylated genes (DMGs). A gene interation network was also generated including DEGs and DMGs, and common biological pathways were identified.
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| Overall design |
RNA/DNA were extracted from human sural nerves of type 2 diabetic patients with neuropathy and sequenced. Samples were initially grouped based on changes in myelinated fiber density (dMFD) over 52 weeks, representing nerve regeneration and degeneration and divided into three groups (regenerators with high nerve regeneration, degenerator with high nerve degeneration, and intermediate for all others) as described in a previous publication by our group (PMID: 24101696). However, unbiased clustering of the expression data in this study identifed three distinct groups, which were significantly different in terms of HbA1c levels (Group1: 8.66 +/- 1.59; Group2: 7.77 +/- 1.43; Group3: 8.67 +/- 1.44). Reduced representation bisulfate sequencing (RRBS) were also performed on the same sural nerve biopsies, belonging to Group1 and Group2.
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| Contributor(s) |
Hur J, Guo K, Feldman EL |
| Citation(s) |
32787975, 38556110 |
| |
| Submission date |
Apr 03, 2020 |
| Last update date |
Jun 20, 2024 |
| Contact name |
Junguk Hur |
| E-mail(s) |
junguk.hur@med.und.edu
|
| Organization name |
University of North Dakota
|
| Department |
Biomedical Sciences
|
| Street address |
1301 N. Columbia Rd. Stop 9037
|
| City |
Grand Forks |
| State/province |
ND |
| ZIP/Postal code |
58202-9037 |
| Country |
USA |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (53)
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| This SubSeries is part of SuperSeries: |
| GSE148061 |
Genome-Wide Profiling of DNA Methylation and Gene Expression Identifies Candidate Genes for Human Diabetic Neuropathy |
|
| Relations |
| BioProject |
PRJNA622976 |
| SRA |
SRP255170 |
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