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| Status |
Public on Feb 15, 2018 |
| Title |
Cell-type-specific Brain Methylomes Profiled via Ultralow-input Microfluidics |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
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| Summary |
Methylomic studies require substantial amounts of DNA samples and this restriction hinders applications involving scarce animal or patient samples with direct biomedical relevance. Here we report a microfluidics-based reduced representative bisulfite sequencing protocol, MIcrofluidic Diffusion-based RRBS (MID-RRBS), that permits methylomic profiling with sub-1 ng starting DNA. Using this technology, we studied DNA methylation in NeuN+ and NeuN- fractions isolated from mouse cerebellum, revealing cell-type specific methylomic patterns. We also studied the DNA methylation in NeuN+ nuclei isolated from clozapine or vehicle treated mouse frontal cortex.
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| Overall design |
We examined genome-wide DNA methylation profiles of GM12878 cell line (with starting DNA sample amounts in the range of 0.3-10 ng and of single cells), NeuN+ and NeuN- fractions from mouse cerebellum (with starting DNA sample amounts of 0.5 or 10 ng) using MID-RRBS. We generated RNA-seq data on NeuN+ and NeuN- nuclei from mouse cerebellum. We also included MID-RRBS and RNA-seq data obtained on homogenates from mouse cerebellum. Finally, we generated MID-RRBS and RNA-seq data on NeuN+ nuclei isolated from clozapine or vehicle treated mouse frontal cortex.
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| Contributor(s) |
Ma S, Lu C |
| Citation(s) |
29963329 |
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Sai Ma, Mario de la Fuente Revenga, Zhixiong Sun, Chen Sun, Travis W. Murphy, Hehuang Xie, Javier González-Maeso and Chang Lu. Cell-type-specific brain methylomes profiled via ultralow-input microfluidics. Nature Biomedical Engineering 2018;2:183-194. doi:10.1038/s41551-018-0204-3
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| Submission date |
Oct 13, 2016 |
| Last update date |
Jul 25, 2021 |
| Contact name |
Chang Lu |
| E-mail(s) |
changlu@vt.edu
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| Phone |
5402318681
|
| Organization name |
Virginia Tech
|
| Department |
Chemical Engineering
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| Lab |
Chang Lu
|
| Street address |
235 Goodwin Hall, 635 Prices Fork Road, Virginia Tech
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| City |
Blacksburg |
| State/province |
VA |
| ZIP/Postal code |
24061 |
| Country |
USA |
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| Platforms (2) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
| GPL21103 |
Illumina HiSeq 4000 (Mus musculus) |
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| Samples (94)
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| Relations |
| BioProject |
PRJNA348345 |
| SRA |
SRP091511 |
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