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Sample GSM1054583 Query DataSets for GSM1054583
Status Public on Feb 01, 2013
Title male DKO#51 versus male WT#6 Replicate 1
Sample type RNA
 
Channel 1
Source name male WT ESC
Organism Mus musculus
Characteristics background strain: C57/BL/6
gender: male
genotype: wildtype
Treatment protocol Feeders were separated by preplating on gelatin coated platesprior to mRNA extraction.
Growth protocol Mouse embryonic stem cells were cultured on gamma irridiated feeders in LIF contianing medium.
Extracted molecule total RNA
Extraction protocol RNA was extracted using Qiagen RNAeasy Kit
Label Cy3
Label protocol Cy3 and Cy5-labeled cRNA was prepared using the Low Input Quick Amp labeling kit (Agilent) starting with 200ng of total RNA
 
Channel 2
Source name male Tet1 Tet2 DKO ESC
Organism Mus musculus
Characteristics genotype: Tet1/Tet2 double knockout
background strain: C57/BL/6
gender: male
Treatment protocol Feeders were separated by preplating on gelatin coated platesprior to mRNA extraction.
Growth protocol Mouse embryonic stem cells were cultured on gamma irridiated feeders in LIF contianing medium.
Extracted molecule total RNA
Extraction protocol RNA was extracted using Qiagen RNAeasy Kit
Label Cy5
Label protocol Cy3 and Cy5-labeled cRNA was prepared using the Low Input Quick Amp labeling kit (Agilent) starting with 200ng of total RNA
 
 
Hybridization protocol Agilent V2 Mouse 4x44k expression arrays were hybridized and washed according to manufacturer's instructions
Scan protocol Agilent DNA microarray scanner was used following manufaturer's instructions
Data processing Data were normalized within array by loess normalization and between arrays by quantile normalization of average intensities (“Aquantile”) using Bioconductor. Probes for the same gene were summarized by mean and technical replicas were combined by average
 
Submission date Dec 18, 2012
Last update date Feb 01, 2013
Contact name Inmaculada Barrasa
E-mail(s) wibr-bioinformatics@wi.mit.edu
Organization name Whitehead Institute
Street address Nine Cambridge Center
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
 
Platform ID GPL11202
Series (1)
GSE42991 Gene expression profiles of Tet1 knockout (T1KO), Tet2 knockout (T2KO) and Tet1/Tet2 double knockout (DKO) mouse embryonic stem cells.

Data table header descriptions
ID_REF
VALUE log2 (Cy5/Cy3) after loess and Aquantile normalization. Probes for the same gene are summarized by mean.

Data table
ID_REF VALUE
GE_BrightCorner 0.127186559
DarkCorner -0.095519194
A_55_P1989846 0.813771027
A_55_P1991598 0.053425923
A_55_P2022211 -0.26908862
A_55_P1980764 0.093901105
A_55_P1964375 0.156736832
A_51_P128876 -0.868440585
A_55_P2121042 0.058293123
A_52_P219230 0.071873334
A_51_P207591 -0.619929093
A_55_P2131920 0.068689555
A_55_P2404223 0.049965242
A_55_P2101944 0.28277235
A_52_P358860 0.338549516
A_51_P119031 0.771491212
A_51_P309854 -0.301730072
A_51_P343900 -0.032091746
A_51_P234359 0.772736824
A_51_P487813 0.919851623

Total number of rows: 31595

Table truncated, full table size 801 Kbytes.




Supplementary file Size Download File type/resource
GSM1054583_252665513881_201205041051_S01_GE2-v5_10_Apr08_1_1.txt.gz 15.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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