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Sample GSM1054586 Query DataSets for GSM1054586
Status Public on Feb 01, 2013
Title female DKO#60 versus female WT#7 Replicate 1
Sample type RNA
 
Channel 1
Source name female WT ESC
Organism Mus musculus
Characteristics background strain: C57/BL/6
gender: female
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 female Tet1 Tet2 DKO ESC
Organism Mus musculus
Characteristics genotype: Tet1/Tet2 double knockout
background strain: C57/BL/6
gender: female
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 0.143621265
DarkCorner -0.046257664
A_55_P1989846 0.12174677
A_55_P1991598 0.058709246
A_55_P2022211 1.223174613
A_55_P1980764 0.110097763
A_55_P1964375 0.123558377
A_51_P128876 -1.024999046
A_55_P2121042 -0.033644843
A_52_P219230 -0.0362874
A_51_P207591 -0.262839046
A_55_P2131920 0.871354924
A_55_P2404223 -0.582422797
A_55_P2101944 0.172780017
A_52_P358860 0.368290715
A_51_P119031 0.932542605
A_51_P309854 -0.241355621
A_51_P343900 -0.46215738
A_51_P234359 -0.949244426
A_51_P487813 1.516730932

Total number of rows: 31595

Table truncated, full table size 801 Kbytes.




Supplementary file Size Download File type/resource
GSM1054586_252665513882_201205041059_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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