NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1565375 Query DataSets for GSM1565375
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

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

Data table
ID_REF VALUE
AB000096 593.4553
AB000490 666.7253
AB001425 347.6531
AB001435 436.6756
AB001539 892.9103
AB001750 207.9864
AB001926 173.0655
AB003502 76.0378
AB004048 324.4151
AB005662 9695.4302
AB005665 214.4676
AB005909 138.1404
AB006034 70.0335
AB006103 126.1559
AB007407 227.567
AB008928 303.1479
AB009369 285.2046
AB010088 331.0863
AB010122 363.8231
AB011499 264.8509

Total number of rows: 44171

Table truncated, full table size 789 Kbytes.




Supplementary file Size Download File type/resource
GSM1565375_537770A05_2013-10-30_09-47_Area1_532.pair.gz 2.7 Mb (ftp)(http) PAIR
GSM1565375_537770A05_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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap
External link. Please review our privacy policy.