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| Status |
Public on Aug 20, 2019 |
| Title |
DNA methylation changes in regional lung macrophages are associated with metabolic differences |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by array
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| Summary |
A flexible fiberoptic bronchoscope was inserted trans-orally and advanced through the vocal cords of subjects. Brochoalveolar lavage (BAL) fluid was obtained from tertiary airways in the right upper and lower lobes.
The BAL procedure was performed sequentially in the right upper lobe (RUL) and right lower lobe (RLL) with 20 ml of sterile saline followed by 10 ml of air and this was repeated for a total of 5 times per airway. BAL fluid was then filtered through 2-layer gauze, centrifuged, and washed twice in 0.9% NaCl. Cells were counted with a T10 automated cell counter.
Cytospins were performed using a Shandon Cytospin 3 centrifuge. 75,000 cells resuspended in 200 l of 0.9% NaCl were loaded into a cytology funnel and centrifuged for 10 mins. Cells were allowed to air dry and processed for viewing via Hema 3 Stat pack.
One pair of samples (GEO accessions GSM3610354 [H_1_RLL] and GSM3610362 [H_1_RUL]) from our previous publication, collected and measured in the same manner, was also included in our present analysis.
DNA was extracted from lung macrophages via Qiagen DNeasy Blood and Tissue Kit. DNA was quantitated on a Qubit 3.0 Fluorometer. Bisulfite conversion of DNA was performed using the Zymo EZ DNA methylation kit. The Illumina MethylationEPIC array hybridization and scanning were performed at the University of Southern California Molecular Genomics Core.
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| Overall design |
BAL fluids from 12 heathy subjects' right upper and lower lung lobe were acquired. A pair of upper and lower-lobe samples from one additional subject (GEO accessions GSM3610354 and GSM3610362) used as a healthy control in our previously published cystic fibrosis manuscript (Chen & Armstrong et al. 2018) was also included in the present analysis.
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| Contributor(s) |
Armstrong DA, Chen Y |
| Citation(s) |
31356157 |
| Submission date |
Jun 11, 2019 |
| Last update date |
Aug 20, 2019 |
| Contact name |
Youdinghuan Chen |
| E-mail(s) |
Youdinghuan.Chen.GR@dartmouth.edu
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| Organization name |
Dartmouth College
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| Department |
Epidemiology
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| Street address |
Hinman Box 7650
|
| City |
Lebanon |
| State/province |
NH |
| ZIP/Postal code |
03756 |
| Country |
USA |
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| Platforms (1) |
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| Samples (24)
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| Relations |
| BioProject |
PRJNA548341 |
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