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Sample GSM990728 Query DataSets for GSM990728
Status Public on Oct 28, 2012
Title WT Cardiomyocytes 72hr after PBS rep4
Sample type RNA
 
Source name WT Cardiomyocytes 72hr after PBS
Organism Mus musculus
Characteristics strain background: 129SvEv/C57BL/6
gender: male
age: 6 weeks
genotype/variation: wild type
injected with: PBS (i.p.)
tissue: heart
cell type: primary cardiomyocytes
Treatment protocol Mice were first injected with doxorubicin (25mg/kg, i.p.) or PBS (i.p.). Hearts were removed 16hr or 72 hr after injection. Live cardiomyocytes were isolated from the heart immediately by using a Langendorff aparatus.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from the isolated cardiomyocytes with TRIZOL reagent (Invitrogen), RNA was then purified with RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
Label Cy3
Label protocol One hundred nanograms of each total RNA sample were used. To produce Cy3-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.
 
Hybridization protocol The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 600 ng Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65 °C) to Agilent Whole Mouse Genome Oligo Microarrays 8x60K using Agilent’s recommended hybridization chamber and oven
Scan protocol Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies)
Description Gene expression 72 hr after PBS injection (i.p.)
72 hr WT Ctr4
Data processing The Agilent Feature Extraction Software (FES, Version 10.7.3.1) was used to read out and process the microarray image files. The software determines feature intensities (including background subtraction), rejects outliers and calculates statistical confidences. For determination of differential gene expression FES derived output data files were further analyzed using the Rosetta Resolver gene expression data analysis system (Rosetta Biosoftware, Version 7.2)
 
Submission date Aug 22, 2012
Last update date Oct 28, 2012
Contact name Sui Zhang
Organization name U.T. M.D. Anderson Cancer Center
Department Cardiology
Street address 1400 Pressler St.
City Houston
State/province TX
ZIP/Postal code 77025
Country USA
 
Platform ID GPL13912
Series (1)
GSE40289 Gene expression in the wildtype and top2b-deleted cardiomyocytes with or without doxorubicin treatment

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
4 0.237954
5 2.758758
6 0.385527
7 0.238703
8 179.355308
9 0.238974
10 0.239042
11 0.413679
12 0.239062
13 6.805373
14 101.016422
15 0.738625
16 0.551949
17 175.622338
18 5.010987
19 43.169641
20 1641.546707
21 5.792742
22 1.224764
23 57.964487

Total number of rows: 59305

Table truncated, full table size 876 Kbytes.




Supplementary file Size Download File type/resource
GSM990728_252800512213_S01_GE1_107_Sep09_1_1.txt.gz 11.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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