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Sample GSM1712149 Query DataSets for GSM1712149
Status Public on Sep 11, 2015
Title ES-CM-siScr-2
Sample type RNA
Source name embryonic stem cells-derived cardiomyocytes treated with si-Scramble
Organism Mus musculus
Characteristics cell line: CGR8
transfection: siRNA-Scramble
Treatment protocol The cells were transfected with siScr or siErbB4 for 48 hours using Pepmute transfection agent
Growth protocol Mouse embryonic stem cells-derived cardiomyocytes were cultured in DMEM-LG+2%FBS. The cultures were incubated for 6 or 24 hours at 37 ºC in a humidified incubator with 5% CO2.
Extracted molecule total RNA
Extraction protocol RNA were extracted using RNEasy Plus Mini Kit with DNAse treatment
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
Hybridization protocol 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse GE 4*44K v2 Microarrays (G4846A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) at 535 nm for Cy3.
Description Gene expression after transfected with si-Scr
Data processing The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1_107_Sep0 and Grid: 026655_D_F_20130207) to obtain background subtracted and spatially detrended Processed Signal intensities.
GeneSpring GX v12.6 (Agilent Technologies) was used to analyze the expression profiles obtained after microarray hybridization. The feature extraction files from all the samples were uploaded to GeneSpring. Follow by Percentile Shift Normalization.
Submission date Jun 15, 2015
Last update date Sep 11, 2015
Contact name Desy S Lee
Organization name NCKU
Street address University Road
City Tainan
ZIP/Postal code 701
Country Taiwan
Platform ID GPL11202
Series (1)
GSE69897 Gene expression profile of mouse embryonic stem cells derived cardiomyocytes following the knockdown of ErbB4

Data table header descriptions
VALUE normalized signal

Data table
GE_BrightCorner 4.532716
DarkCorner -8.0395565
A_55_P1989846 -2.4635105
A_55_P1991598 -6.484606
A_55_P2022211 3.03123
A_55_P1980764 -6.0496187
A_55_P1964375 2.0922527
A_51_P128876 -0.66040134
A_55_P2121042 -6.1604776
A_52_P219230 -7.6674232
A_51_P207591 -1.8881693
A_55_P2131920 -1.8769865
A_55_P2404223 -1.6580696
A_55_P2101944 2.6068363
A_52_P358860 0.7494345
A_51_P119031 0.7590866
A_51_P309854 -0.5578642
A_51_P343900 2.262045
A_51_P234359 -0.8214693
A_51_P487813 1.6791344

Total number of rows: 39485

Table truncated, full table size 924 Kbytes.

Supplementary file Size Download File type/resource
GSM1712149_Si-Scr-2.txt.gz 2.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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