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Sample GSM810501 Query DataSets for GSM810501
Status Public on Nov 02, 2012
Title Eed-/- male TS cells H3K27me3 ChIP DNA
Sample type genomic
 
Channel 1
Source name Eed-/- male TS cells H3K27me3 ChIP DNA
Organism Mus musculus
Characteristics genotype: XWT/XGFP
cell type: Trophoblast Stem cells isolated from E3.5 blastocysts
chip antibody: H3K27me3
chip antibody manufacturer: Millipore
chip antibody catalog #: #17-622
gender: male
Treatment protocol No treatment
Extracted molecule genomic DNA
Extraction protocol Chromatin was fixed in 1% formaldehyde for 10 min, sheared to 200-700 bp using a Bioruptor (Diagenode). It was immunoprecipitated using the indicated antibody. Genomic DNA was isolated from the precipitated material as well as from the sheared chromatin input by phenol extraction and ethanol precipitation. The ChIP material was amplified using whole genome amplification (WGA-2, SIGMA). For detailed protocol see (Navarro et al., Genes Dev, 2005).
Label Cy5
Label protocol Labelling was performed by NimbleGen using 4 ug of ChIP DNA and 4 ug of Input DNA (http://www.nimblegen.com/products/chip/tutorial.html)
 
Channel 2
Source name Input DNA from Eed-/- male TS cells
Organism Mus musculus
Characteristics genotype: XWT/XGFP
cell type: Trophoblast Stem cells isolated from E3.5 blastocysts
chip antibody: none, input DNA
gender: male
Treatment protocol No treatment
Extracted molecule genomic DNA
Extraction protocol Chromatin was fixed in 1% formaldehyde for 10 min, sheared to 200-700 bp using a Bioruptor (Diagenode). It was immunoprecipitated using the indicated antibody. Genomic DNA was isolated from the precipitated material as well as from the sheared chromatin input by phenol extraction and ethanol precipitation. The ChIP material was amplified using whole genome amplification (WGA-2, SIGMA). For detailed protocol see (Navarro et al., Genes Dev, 2005).
Label Cy3
Label protocol Labelling was performed by NimbleGen using 4 ug of ChIP DNA and 4 ug of Input DNA (http://www.nimblegen.com/products/chip/tutorial.html)
 
 
Hybridization protocol Hybridisation was performed by NimbleGen (http://www.nimblegen.com/products/chip/)
Scan protocol Scanning was performed by NimbleGen (http://www.nimblegen.com/products/chip/)
Description specimen described in Kalantry S. et al., Nat Cell Biol, 2006
EED_XY_H3K27me3
Data processing Reproducibility and quality control of the data were assessed using the “R” package combined with an algorithm especially developed for ChIP-on-Chip data analysis of histone modifications (http://www.epigenome-noe.net/WWW/researchtools/protocol.php?protid=43). Briefly, the global hybridisation patterns across each array were controlled by MA-plotting of all the probe signals on the array and by calculating the Pearson correlation coefficients between pairs of replicates (all the coefficients were > 0.8). The two replicates showing the highest Pearson correlation coefficient were used for further analysis. We applied a Lowess normalisation to each dataset and the “SAM” algorithms to determined statistically enriched probe (Tusher et al., PNAS, 2001). A VSN (variance stabilization) normalisation of each array was also performed independently, then a SAM algorithm and a lfdr > 0,2 (local false discovery rate probability test) to determine the significance of enrichment of each probel were applied (data not included in this submission but available upon request).
 
Submission date Oct 05, 2011
Last update date Nov 02, 2012
Contact name Celine Morey
E-mail(s) [email protected]
Phone +33 1 57278930
Organization name UMR7216-Epigenetics and stem cell
Department University Paris 7
Lab Non-coding RNAs, differentiation and development
Street address 35 rue Hélène Brion
City Paris
ZIP/Postal code 75013
Country France
 
Platform ID GPL14676
Series (1)
GSE32655 H3K27me3 profiles along the length of the X chromosome in trophoblast stem (TS) cells, ChIP-chip

Data table header descriptions
ID_REF
VALUE log2 ratio IP/IN
PRE_VALUE ratio IP/IN

Data table
ID_REF VALUE PRE_VALUE
MMUS36_CHR17CHR17P004657287 -0.8890 0.54
MMUS36_CHR17CHR17P004657502 -1.0000 0.50
MMUS36_CHR17CHR17P004657742 -0.5146 0.70
MMUS36_CHR17CHR17P004657972 -0.5778 0.67
MMUS36_CHR17CHR17P004658197 -1.3219 0.40
MMUS36_CHR17CHR17P004658561 -0.8110 0.57
MMUS36_CHR17CHR17P004658701 -1.1203 0.46
MMUS36_CHR17CHR17P004658928 -1.0893 0.47
MMUS36_CHR17CHR17P004659158 -1.4739 0.36
MMUS36_CHR17CHR17P004659400 -1.5146 0.35
MMUS36_CHR17CHR17P004659698 -1.8890 0.27
MMUS36_CHR17CHR17P004659981 -0.9714 0.51
MMUS36_CHR17CHR17P004660521 -1.4344 0.37
MMUS36_CHR17CHR17P004660661 -0.4540 0.73
MMUS36_CHR17CHR17P004660876 -1.0000 0.50
MMUS36_CHR17CHR17P004661106 -1.7370 0.30
MMUS36_CHR17CHR17P004661348 -2.1203 0.23
MMUS36_CHR17CHR17P004661648 -1.5995 0.33
MMUS36_CHR17CHR17P004661873 -1.1844 0.44
MMUS36_CHR17CHR17P004662088 -0.4344 0.74

Total number of rows: 388000

Table truncated, full table size 14875 Kbytes.




Supplementary file Size Download File type/resource
GSM810501_31136002_532.pair.gz 5.8 Mb (ftp)(http) PAIR
GSM810501_31136002_635.pair.gz 5.7 Mb (ftp)(http) PAIR
Processed data included within Sample table

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