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Sample GSM887838 Query DataSets for GSM887838
Status Public on Jun 24, 2013
Title WTG4_ES_DexPlus_12h_rep1
Sample type RNA
 
Source name mouse wild-type Gata4GR (WTG4) ES cells, +Dex, 12hr, replicate 1
Organism Mus musculus
Characteristics cell line: Line J1G4.211
genotype/variation: wild-type, stably expressing Gata4-glucocorticoid receptor ligand binding domain fusion gene
cell type: embryonic stem (ES) cells differentiating to primitive endoderm cells
dexamethasone: yes
time: 12h
Treatment protocol 100 nM dexamethasone (Dex) was added to ES cells stably expressing Gata4GR. The cells were recovered by trypsinization after 12 hours after addition of Dex, and used for RNA preparation.
Growth protocol ES cells were cultured in Glasgow Minimum Essential Medium (GMEM, Sigma) supplemented with 10% fetal calf serum (FCS), 0.1 mM nonessential amino acids (Invitrogen), 1 mM sodium pyruvate, 0.1 mM 2-mercaptoethanol, and 2000 U/ml leukemia inhibitory factor (LIF) on gelatinized culture dishes without feeder cells.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated by using the QIAshredder and the RNeasy Plus Micro Kit with gDNA Eliminator column (Qiagen) according to the manufacturer's protocols. RNA was quantified and quality controlled using the NanoDrop ND-1000 Spectrophotometer (Thermo) and the 2100 Bioanalyzer (Agilent).
Label Cy3
Label protocol Amplification and Cy3 labeling of RNA was prepared from 50 ng of RNA using the Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions (G4140-90040 One-Color Microarray-Based Gene Expression Analysis Protocol Version 6.5). Purification of Cy3-labeled cRNA was performed using the RNeasy Mini Kit (Qiagen). Quantity, quality and dye incorporation of Cy3-labeled cRNA were checked using the NanoDrop ND-1000 Spectrophotometer (Thermo) and the 2100 Bioanalyzer (Agilent).
 
Hybridization protocol 600 ng of Cy3-labeled cRNA was hybridized in Agilent hybridization chambers for 17 hours at 65 degrees C and 10 rpm according to the manufacturer's instructions (G4140-90040 One-Color Microarray-Based Gene Expression Analysis Protocol Version 6.5).
Scan protocol Slide scanning was performed using the Agilent DNA Microarray Scanner G2505C with 3 um resolution and 20-bit dynamic range.
Description Gene expression data from wild-type Gata4GR ES cells diffentiating to primitive endoderm cells with 12hr-culture in the presence of dexamethasone to activate Gata4GR transgene
Data processing The scanned images were processed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid 028005_D_F_20110406) to generate background subtracted and spatially detrended green Processed Signal intensities. Normalize signal intensities were obtained by a) removal of data of control probes, b) log2 transformation, and c) quantile normalization, which was performed using the normalizeQuantiles function of the limma package of the R.
 
Submission date Mar 06, 2012
Last update date Jun 24, 2013
Contact name Yuichi Kumaki
E-mail(s) kuma@cdb.riken.jp
Organization name RIKEN
Department Center for Developmental Biology
Street address 2-2-3 Minatojima-minamimachi, Chuo-ku
City Kobe
ZIP/Postal code 650-0047
Country Japan
 
Platform ID GPL13912
Series (1)
GSE36313 DNA Methylation Restricts Lineage-Specific Functions of Transcription Factor Gata4 during Embryonic Stem Cell Differentiation

Data table header descriptions
ID_REF
VALUE Quantile normalized log2 signal

Data table
ID_REF VALUE
1 null
2 null
3 null
4 1.55311
5 6.85518
6 2.27478
7 1.56509
8 10.4419
9 1.56935
10 4.80955
11 4.10152
12 1.57378
13 6.99312
14 11.9879
15 1.57502
16 1.57472
17 12.4459
18 7.37072
19 10.3708
20 16.2678

Total number of rows: 62976

Table truncated, full table size 832 Kbytes.




Supplementary file Size Download File type/resource
GSM887838_DKOG4_087_US91403665_252800511253_S03_GE1_107_Sep09_1_3.txt.gz 11.8 Mb (ftp)(http) TXT
Processed data included within Sample table

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