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Status |
Public on Nov 01, 2016 |
Title |
C57, saline 2 |
Sample type |
RNA |
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|
Source name |
prefrontal cortex, saline treatment
|
Organism |
Mus musculus |
Characteristics |
strain/background: C57BL/6J tissue: prefrontal cortex treatment: saline
|
Treatment protocol |
Mice were treated with saline or morphine.
|
Growth protocol |
Not applicable; these are tissue samples.
|
Extracted molecule |
total RNA |
Extraction protocol |
RNA was prepared using the miRNeasy kit (Qiagen, Valencia, CA) following the manufacturer's recommendations. The protocol includes homogenization of prefrontal cortex samples, and an on-column DNase digestion. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
|
Label |
Cy3
|
Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 250 ng RNA using Agilent's miRNA Complete Labeling according to the manufacturer's instructions. T4 RNA ligase and Cy-3-pCp were used for labeling the miRNA samples. The labeled RNA samples were purified by Micro Bio-Spin 6 column.
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Hybridization protocol |
Cy3-labeled miRNA samples were hybridized in a reaction volume of 45 µl containing 1x Hi-PRM hybridization buffer and 1x GE blocking agent following the manufacturer's instructions. The mixed samples were hybridized to Agilent Human miRNA Microarrays (G4112A) for 20 hours at 55°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 5 minute at room temperature with Gene Expression Wash Buffer 1 (Agilent) and 5 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
|
Scan protocol |
Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2505B) using one color scan setting for 8x15k array slides (scan area: 61 x 21.6 mm, scan resolution: 5 µm, Dye channel: Green, Green PMT: XDR Hi 100%, Lo 5%).
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Description |
Prefrontal cortex from saline-treated C57 mouse. C57_S2
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Data processing |
The scanned images were analyzed with Feature Extraction Software 9.5.3 (Agilent) using default parameters for miRNA array to obtain background subtracted and spatially detrended Processed Signal intensities. The feature extraction files were imported to Agilent's GeneSpring program for data analysis. The quantile normalization and log transformation were applied to get the normalized data across the 8 arrays.
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Submission date |
Dec 10, 2015 |
Last update date |
Nov 01, 2016 |
Contact name |
Bi-Dar Wang |
E-mail(s) |
wangbi@gwu.edu
|
Phone |
202-994-3543
|
Fax |
202-994-2870
|
Organization name |
The George Washington University Medical Center
|
Department |
Pharmacology and Physiology
|
Street address |
2300 I street, NW
|
City |
Washington |
State/province |
DC |
ZIP/Postal code |
20037 |
Country |
USA |
|
|
Platform ID |
GPL8824 |
Series (1) |
GSE75893 |
MicroRNA expression profiling of prefrontal cortex samples from C57 mice treated with saline or morphine |
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