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Sample GSM1098610 Query DataSets for GSM1098610
Status Public on May 01, 2013
Title ESCs_AllStars_rep1
Sample type RNA
 
Source name VV3 ESCs, control siRNA transfected
Organism Mus musculus
Characteristics strain/background: 129SV
gender: male
cell line: VV3
cell type: embryonic stem cells (ESCs)
sirna: non-silencing negative control
Treatment protocol ESCs were transfected with non-silencing negative control siRNA (AllStars) using Lipofectamine RNAiMAX. After 3 days culture, the live and single cells were purified using FACS from the ESCs.
Growth protocol Cells were cultured with ESCs medium with 14% KSR, 1% FBS and LIF at 37 ÂșC in a humidified incubator with 5% CO2.
Extracted molecule total RNA
Extraction protocol Total RNA was purified using the RNeasy micro kit according to the manufacturer's instructions.
Label Cy3
Label protocol Cy3-labeled cRNA samples were prepared using the Agilent Low Input Quick Amp Labeling Kit (one-color) (5190-2305) and RNA Spike-In Kit (one-color) (5188-5282) according to the manufacturer's instructions. Input was 100 ng of total RNA from each sample.
 
Hybridization protocol 1.65ug of Cy3-labelled cRNAs from each sample were fragmented and hybridized to microarrays according to the manufacturer's instructions using the Gene Expression Hybridization kit (Agilent 5188-5242) and Agilent hybridization oven. After hybridization, microarrays were washed using the Gene Expression Wash Pack (Agilent 5188-5327).
Scan protocol The microarrays were scanned using the Agilent DNA microarray scanner (Agilent G2505C); the spot signals were quantified using Feature Extraction software.
Description Gene expression of negative control siRNA-transfected VV3 mouse ESCs.
Data processing Data was normalized and analyzed by GeneSpring GX (Agilent).
 
Submission date Mar 14, 2013
Last update date May 01, 2013
Contact name Ikuma Maeda
E-mail(s) ikuma@idac.tohoku.ac.jp
Phone +81-22-717-8572
Fax +81-22-717-8573
Organization name Institute of Development, Aging and Cancer, Tohoku University
Lab Cell Resource Center for Biomedical Research
Street address 4-1 Seiryomachi, Aoba-ku
City Sendai
State/province Miyagi
ZIP/Postal code 980-8575
Country Japan
 
Platform ID GPL11202
Series (1)
GSE45181 Max is a repressor of germ-cell-related gene expression in mouse embryonic stem cells

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
GE_BrightCorner 0.4027071
DarkCorner 0
A_55_P1989846 0.07570505
A_55_P1991598 -0.3013687
A_55_P2022211 0.11131668
A_55_P1980764 0.9478731
A_55_P1964375 -0.052527428
A_51_P128876 0.14512157
A_55_P2121042 0
A_52_P219230 0
A_51_P207591 1.5499496
A_55_P2131920 0
A_55_P2404223 0
A_55_P2101944 0.30577946
A_52_P358860 -0.047607422
A_51_P119031 0.023758888
A_51_P309854 0.003534794
A_51_P343900 0
A_51_P234359 1.0978851
A_51_P487813 0.41788864

Total number of rows: 39485

Table truncated, full table size 904 Kbytes.




Supplementary file Size Download File type/resource
GSM1098610_252665511678_1.txt.gz 2.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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