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Sample GSM1224049 Query DataSets for GSM1224049
Status Public on Jun 01, 2014
Title F3_H3K27me3_rep1
Sample type genomic
 
Channel 1
Source name wildtype female TS cells H3K27me3 ChIP DNA
Organism Mus musculus
Characteristics strain: Htz 129.Pgk1a/129
genotype/variation: XHprt-/XWT
gender: female
cell type: Trophoblast Stem cells isolated from E3.5 blastocysts
chip antibody: H3K27me3
chip antibody vendor: Millipore
chip antibody cat. #: 17-622
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)
 
Channel 2
Source name input DNA from wildtype female TS cells H3K27me3 ChIP DNA
Organism Mus musculus
Characteristics strain: Htz 129.Pgk1a/129
genotype/variation: XHprt-/XWT
cell type: Trophoblast Stem cells isolated from E3.5 blastocysts
chip antibody: none, input DNA
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)
 
 
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 Sample 3
Data processing Reproducibility and quality control of the data were assessed using the “R” software 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 Sep 04, 2013
Last update date May 05, 2015
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)
GSE50587 H3K27me3 and H3K4me2 profiles along the length of the X chromosome in trophoblast stem (TS) cells and Extra-embryonic endoderm stem cells (XEN), ChIP-chip
Relations
Reanalyzed by GSM1674751

Data table header descriptions
ID_REF
VALUE Lowess normalised ratio IP/IN

Data table
ID_REF VALUE
MMUS36_CHR17CHR17P004657287 1.228529283
MMUS36_CHR17CHR17P004657502 0.728680827
MMUS36_CHR17CHR17P004657742 1.529238024
MMUS36_CHR17CHR17P004657972 0.840014202
MMUS36_CHR17CHR17P004658197 0.690878181
MMUS36_CHR17CHR17P004658561 0.798942764
MMUS36_CHR17CHR17P004658701 0.737985233
MMUS36_CHR17CHR17P004658928 0.680657883
MMUS36_CHR17CHR17P004659158 0.970704638
MMUS36_CHR17CHR17P004659400 0.938339356
MMUS36_CHR17CHR17P004659698 0.552197841
MMUS36_CHR17CHR17P004659981 0.626045269
MMUS36_CHR17CHR17P004660521 0.339952902
MMUS36_CHR17CHR17P004660661 0.521253047
MMUS36_CHR17CHR17P004660876 0.653426554
MMUS36_CHR17CHR17P004661106 0.293889503
MMUS36_CHR17CHR17P004661348 0.444873512
MMUS36_CHR17CHR17P004661648 0.993379156
MMUS36_CHR17CHR17P004661873 0.711108157
MMUS36_CHR17CHR17P004662088 0.629539138

Total number of rows: 388000

Table truncated, full table size 14457 Kbytes.




Supplementary file Size Download File type/resource
GSM1224049_8155802_532.pair.gz 6.2 Mb (ftp)(http) PAIR
GSM1224049_8155802_635.pair.gz 6.1 Mb (ftp)(http) PAIR
Processed data included within Sample table

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