|
Status |
Public on May 23, 2016 |
Title |
WT-METH-1 [gene expression] |
Sample type |
RNA |
|
|
Source name |
Total RNA from WT-METH Left Ventricle
|
Organism |
Mus musculus |
Characteristics |
genotype/variation: WT treatment: METH strain: C57Bl/6
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc.) and cDNA was synthesized using Superscript Double-Stranded cDNA Synthesis kit (Invitrogen/Life Technologies). cDNA quality was determined using a Spectramax 190 plate reader ( ) for A260 and A280 absorbance determination along with gel electrophoresis.
|
Label |
Cy3
|
Label protocol |
DNA labeling was completed using NimbleGen labeling Kit following their standard operating protocol.
|
|
|
Hybridization protocol |
Hybridization was completed using NimbleGen Hybridization Kit (Cat # 05583683001)following their standard operating protocol.
|
Scan protocol |
Scanning was performed using Roche NimbleGen MS200 Microarray Scanner following the manufacturer's standard protocol.
|
Data processing |
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package (Roche NimbleGen, Inc.).
|
|
|
Submission date |
Dec 15, 2014 |
Last update date |
May 24, 2016 |
Contact name |
William Lewis |
Organization name |
Emory University
|
Department |
Pathology
|
Lab |
Lewis Lab
|
Street address |
101 Woodruff Circle
|
City |
Atlanta |
State/province |
Georgia |
ZIP/Postal code |
30322 |
Country |
USA |
|
|
Platform ID |
GPL15887 |
Series (2) |
GSE64157 |
Methamphetamine and HIV-Tat Alter Murine Cardiac DNA Methylation and Gene Expression [Gene Expression] |
GSE64159 |
Methamphetamine and HIV-Tat Alter Murine Cardiac DNA Methylation and Gene Expression |
|