NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1054585 Query DataSets for GSM1054585
Status Public on Feb 01, 2013
Title male DKO#61 versus male WT#92 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 0.056892621
DarkCorner -0.113612986
A_55_P1989846 0.216688836
A_55_P1991598 0.033637281
A_55_P2022211 0.590837625
A_55_P1980764 -0.021208642
A_55_P1964375 -0.020922672
A_51_P128876 -0.920519784
A_55_P2121042 0.107207786
A_52_P219230 0.050911615
A_51_P207591 -0.259864933
A_55_P2131920 -0.246943646
A_55_P2404223 0.007547127
A_55_P2101944 0.029959596
A_52_P358860 0.321574118
A_51_P119031 0.577119319
A_51_P309854 0.22467114
A_51_P343900 -0.378256152
A_51_P234359 -0.215075414
A_51_P487813 0.351594332

Total number of rows: 31595

Table truncated, full table size 801 Kbytes.




Supplementary file Size Download File type/resource
GSM1054585_252665513881_201205041051_S01_GE2-v5_10_Apr08_1_3.txt.gz 15.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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