NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM889987 Query DataSets for GSM889987
Status Public on Feb 17, 2021
Title Dnmts TKO
Sample type RNA
 
Source name mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- ES cells
Organism Mus musculus
Characteristics cell line: Line 19-1
genotype: Dnmt1-/-Dnmt3a-/-Dnmt3b-/-
cell type: embryonic stem cells (ESCs)
Growth protocol ES cells were cultured in feeder-free conditions in Glasgow Minimum Essential Medium (GMEM) (WAKO) containing 10% FCS (Invitrogen), 1 mM glutamine (WAKO), nonessential amino acid (WAKO) and 0.1 mM mercaptoethanol (WAKO) and supplemented with LIF (WAKO).
Extracted molecule total RNA
Extraction protocol Total RNA was isolated by TRIZOL Reagent (Invitrogen) and purified using 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 Dnmt1-/-Dnmt3a-/-Dnmt3b-/- ES cells
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 08, 2012
Last update date Feb 17, 2021
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)
GSE36371 Expression data from mouse wild type, PRDM14-overexpressing and Dnmts KO embryonic stem cells (ESCs).

Data table header descriptions
ID_REF
VALUE Quantile normalized log2 signal

Data table
ID_REF VALUE
1 null
2 null
3 null
4 1.49888
5 5.52688
6 1.50851
7 1.51258
8 10.5251
9 1.51933
10 5.5187
11 4.07327
12 2.39408
13 6.37052
14 11.6025
15 1.53097
16 1.53151
17 12.3762
18 7.65642
19 10.3746
20 16.2187

Total number of rows: 62976

Table truncated, full table size 832 Kbytes.




Supplementary file Size Download File type/resource
GSM889987_PRDM14_010_US91403665_252800511255_S02_GE1_107_Sep09_2_4.txt.gz 11.9 Mb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap