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Sample GSM1565385 Query DataSets for GSM1565385
Status Public on May 23, 2016
Title TatHB-METH-3 [gene expression]
Sample type RNA
 
Source name Total RNA from TatHB-METH Left Ventricle
Organism Mus musculus
Characteristics genotype/variation: TatHB
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

Data table header descriptions
ID_REF
VALUE RMA-normalized, averaged gene-level signal intensity

Data table
ID_REF VALUE
AB000096 675.5752
AB000490 104.3965
AB001425 884.2442
AB001435 265.2371
AB001539 984.633
AB001750 315.2311
AB001926 824.0953
AB003502 108.2128
AB004048 439.2489
AB005662 4297.9635
AB005665 854.4416
AB005909 97.5856
AB006034 76.2824
AB006103 271.4982
AB007407 130.4068
AB008928 129.244
AB009369 335.7476
AB010088 430.9977
AB010122 199.9891
AB011499 337.0033

Total number of rows: 44171

Table truncated, full table size 789 Kbytes.




Supplementary file Size Download File type/resource
GSM1565385_537770A11_2013-10-30_09-47_Area1_532.pair.gz 2.7 Mb (ftp)(http) PAIR
GSM1565385_537770A11_2013-10-30_09-47_Area1_532_RMA.calls.gz 3.7 Mb (ftp)(http) CALLS
Processed data included within Sample table
Processed data provided as supplementary file

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