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| Status |
Public on Sep 22, 2023 |
| Title |
Differential usage of DNA modifications in neurons, astrocytes and microglia [WGoxBS] |
| Organism |
Mus musculus |
| Experiment type |
Methylation profiling by high throughput sequencing
|
| Summary |
Cellular identity is determined, in part, by cell type-specific epigenomic profiles that govern gene expression. Isolation and epigenomic characterization of specific cell types is greatly needed in neuroscience. While single cell DNA modification studies offer promise to answer this question, these approaches suffer from limited genomic coverage and cannot differentiate between methylation and hydroxymethylation. Thus, approaches to isolate and analyze DNA from specific CNS cell populations are needed. Here we validate a temporally controlled in vivo nuclear tagging mouse model (NuTRAP) and isolation (INTACT) of neuronal nucleic acids. Analysis of differential DNA modifications (methylation and hydroxymethylation) and gene expression in neurons, astrocytes, and microglia demonstrates a common regulatory function for DNA modifications that transcends cell type. Insight into the normal function of DNA modifications in genomic regulation is crucial in order to better understand the epigenomic mechanisms underlying disease.
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| |
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| Overall design |
Camk2a-cre/ERT2;NuTRAP; Nuclei isolated via INTACT method- Input, Negative, and Positive Fractions; 4 biological replicates
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| |
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| Contributor(s) |
Tooley KB, Chucair-Elliott AJ, Ocanas SR, Pham KD, Stanford DR, Freeman WM |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Mar 23, 2023 |
| Last update date |
Sep 22, 2023 |
| Contact name |
Kyla Tooley |
| E-mail(s) |
kyla-tooley@omrf.org
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| Organization name |
Oklahoma Medical Research Foundation
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| Department |
Genes and Human Disease
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| Lab |
Dr. Willard Freeman
|
| Street address |
825 NE 13th St
|
| City |
Oklahoma City |
| State/province |
OK |
| ZIP/Postal code |
73104 |
| Country |
USA |
| |
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| Platforms (2) |
| GPL16417 |
Illumina MiSeq (Mus musculus) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (40)
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| This SubSeries is part of SuperSeries: |
| GSE228045 |
Differential usage of DNA modifications in neurons, astrocytes and microglia |
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| Relations |
| BioProject |
PRJNA947923 |
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