NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM615431 Query DataSets for GSM615431
Status Public on May 17, 2011
Title 6301202Col - H3K27me3_Col_II_IP vs H3K27me3_Col_II_INPUT
Sample type genomic
 
Channel 1
Source name H3K27me3_Col_II_INPUT
Organism Arabidopsis thaliana
Characteristics strain: col-0
age: 10 day
tissue: seedling
sample type: input DNA
Treatment protocol no treatment
Growth protocol seedling - 10 days in liquid MS 0.5X at 22 degrees C. Cool white light at 100 uEm-2s-1, 16 hour photoperiod.
Extracted molecule genomic DNA
Extraction protocol Col_II:50ug.
Label Cy5
Label protocol labelling Cy3 and Cy5 indirect, amplification=yes, DNA .
 
Channel 2
Source name H3K27me3_Col_II_IP
Organism Arabidopsis thaliana
Characteristics strain: col-0
age: 10 day
tissue: seedling
antibody: H3K27me3
antibody manufacturer: Upstate
antibody catalog #: 07-449
Treatment protocol no treatment
Growth protocol seedling - 10 days in liquid MS 0.5X at 22 degrees C. Cool white light at 100 uEm-2s-1, 16 hour photoperiod.
Extracted molecule genomic DNA
Extraction protocol Col_II:50ug. antibody: H3K27me3 (Upstate 07-449);
Label Cy3
Label protocol labelling Cy3 and Cy5 indirect, amplification=yes, DNA .
 
 
Hybridization protocol H3K27me3_Col_II_INPUT Cy5 / H3K27me3_Col_II_IP Cy3 : 80pmol.
Scan protocol NimbleGen, Cy3:pmt voltage 532nm,650V,laser power 100%, Cy5:635nm,pmt voltage 700V,laser power 100%
Description arabidopsis thaliana (col-0) - age: 10day dev.stage (Boyes et al. Plant Cell 2001):seedling
Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between
Data processing For the ChIP-chip data we performed a normalization step by an ANOVA model (Kerr et.al,2002) to remove technical biases.Let Yplfts be the log2 intensity of the probe s on the chip p and the array l, with treatment t and fluorochrome f.The considered model is: Yplfts=mu+ap+bl+abpl+cf+acpf+Eplfts, where ap+bl+abpl is the support effect (chip, array and interactions), cf is the fluorochrome effect, acpf is the chip*fluorochrome interaction and the errors Eplfts are centered Gaussian variables.We estimated the parameters of the model and we removed quantified biases from the raw data.The IP and INPUT intensities for each biological replicate were then averaged on the dye-swap to remove gene-specific dye biases.To analyze data, we use ChIPmix, a method proposed by Martin-Magniette et al.(2008) that we have adapted to study several biological replicates simultaneously. The method investigates the relationship between IP and Input by a mixture model of regressions. For a probe, available observation are the two measurements IP and INPUT for the two biological replicates. These latter are assumed to be independent by definition. The (unknown) status of a probe is characterized through a label Z which is 1 if the probe is enriched and 0 if it is normal (not enriched).
 
Submission date Nov 01, 2010
Last update date May 17, 2011
Contact name François ROUDIER
E-mail(s) [email protected]
Organization name Ecole Normale Supérieure de Lyon
Department Biologie
Lab RDP
Street address 46 Allée d'Italie
City Lyon
ZIP/Postal code 69364
Country France
 
Platform ID GPL10919
Series (2)
GSE24836 Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions
GSE25059 h3k27me3_col(c24)-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions

Data table header descriptions
ID_REF ID
VALUE Normalized log ratio base 2 IP/INPUT (INPUT=reference)
Intensity_cy5 Normalized intensity of Ch1(Cy5) = INPUT
Intensity_cy3 Normalized intensity of Ch2(Cy3) = IP
STATUS (0/1) 1 if the FDR.BH < 0.01 and 0 otherwise
FDR.BH The false discovery rate (FDR) were controlled at the 1% level using a Benjamini and Hochberg correction probability

Data table
ID_REF VALUE Intensity_cy5 Intensity_cy3 STATUS FDR.BH
CHR01FS003081602 3.528740038 8.933043862 12.4617839 1 1.00E-07
CHR02FS018529044 3.160093733 8.157777457 11.31787119 1 6.99E-05
CHR01FS008093949 -3.467321309 13.27017014 9.802848831 0 0.999999271
CHR04FS003211426 0.43451046 14.56803309 15.00254355 1 2.52E-07
CHR05FS000047358 0.14093188 10.84567894 10.98661082 0 0.130952091
CHR03FS000946504 -0.12099388 10.98609437 10.86510049 0 0.298121951
CHR01FS010199643 0.80285583 12.31448163 13.11733746 1 4.94E-05
CHR03FS001114922 -0.893456005000001 10.47735519 9.583899185 0 0.928361455
CHR05FS004553529 1.2209656 9.56600719 10.78697279 0 0.042441558
CHR01FS027858601 1.403928988 6.872766049 8.276695037 0 0.752405301
CHR03FS011176169 -0.64770959 12.20984499 11.5621354 0 0.159528831
CHR04FS004887840 1.95655645 10.77338117 12.72993762 1 7.23E-06
CHR04FS003327559 -1.33505809 12.88453338 11.54947529 0 0.334499651
CHR02FS012259362 -0.379408620000001 12.05300502 11.6735964 0 0.131608043
CHR01FS018106495 -1.43403044 11.93509637 10.50106593 0 0.783354659
CHR02FS019488992 -1.82849269 12.38452601 10.55603332 0 0.941890911
CHR05FS023502273 -0.156464526000001 8.819914355 8.663449829 0 0.999998276
CHR02FS003328581 -1.40372333 12.82011819 11.41639486 0 0.412227046
CHR02FS012729152 3.284425865 8.755415855 12.03984172 1 1.23E-06
CHR05FS020332625 -0.984016293 10.42138954 9.437373247 0 0.999998276

Total number of rows: 360718

Table truncated, full table size 23738 Kbytes.




Supplementary file Size Download File type/resource
GSM615431_6301202Col_532.pair.gz 6.0 Mb (ftp)(http) PAIR
GSM615431_6301202Col_635.pair.gz 6.2 Mb (ftp)(http) PAIR
Processed data included within Sample table

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