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Sample GSM1969512 Query DataSets for GSM1969512
Status Public on Nov 01, 2016
Title C57, saline 1
Sample type RNA
 
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.
 
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%).
Description Prefrontal cortex from saline-treated C57 mouse.
C57_S1
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.
 
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

Data table header descriptions
ID_REF
VALUE Batch-corrected, log10-transformed, normalized signal intensity

Data table
ID_REF VALUE
mghv-miR-M1-1
mghv-miR-M1-2 1.155802631
mghv-miR-M1-3
mghv-miR-M1-4
mghv-miR-M1-5
mghv-miR-M1-6
mghv-miR-M1-7-3p
mghv-miR-M1-7-5p
mghv-miR-M1-8
mghv-miR-M1-9
mmu-let-7a 3.757716396
mmu-let-7b 3.785928221
mmu-let-7b* 0.845183768
mmu-let-7c 3.89505719
mmu-let-7c-1*
mmu-let-7c-2*
mmu-let-7d 3.496202265
mmu-let-7d* 0.268819789
mmu-let-7e 3.430032519
mmu-let-7f 3.535037446

Total number of rows: 577

Table truncated, full table size 10 Kbytes.




Supplementary file Size Download File type/resource
GSM1969512_251911910772_S01_1_3_GeneView_C57_S1_n.txt.gz 5.1 Kb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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