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Sample GSM615057 Query DataSets for GSM615057
Status Public on May 17, 2011
Title 12001402ColCvi - H3K27me3_ColxCvi_I_INPUT vs H3K27me3_ColxCvi_I_IP
Sample type genomic
 
Channel 1
Source name H3K27me3_ColxCvi_I_IP
Organism Arabidopsis thaliana
Characteristics strain: colxcvi hybrids
age: 15 day
tissue: seedling
antibody: H3K27me3
antibody manufacturer: Upstate
antibody catalog #: 07-449
sample type: input DNA
Treatment protocol no treatment
Growth protocol seedling - 15 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 ColxCvi_I:20ug. antibody: H3K27me3 (Upstate 07-449);
Label Cy5
Label protocol labelling Cy3 and Cy5 indirect, amplification=yes, DNA .
 
Channel 2
Source name H3K27me3_ColxCvi_I_INPUT
Organism Arabidopsis thaliana
Characteristics strain: colxcvi hybrids
age: 15 day
tissue: seedling
Treatment protocol no treatment
Growth protocol seedling - 15 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 ColxCvi_I:20ug.
Label Cy3
Label protocol labelling Cy3 and Cy5 indirect, amplification=yes, DNA .
 
 
Hybridization protocol H3K27me3_ColxCvi_I_IP Cy5 / H3K27me3_ColxCvi_I_INPUT Cy3 : 80pmol.
Scan protocol NimbleGen, Cy3:pmt voltage 532nm,650V,laser power 100%, Cy5:635nm,pmt voltage 700V,laser power 100%
Description arabidopsis thaliana (colxcvi hybrids) - age: 15day 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) francois.roudier@ens-lyon.fr
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 GPL10920
Series (2)
GSE24836 Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions
GSE25050 h3k27me3_colxcvi-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) = IP
Intensity_cy3 Normalized intensity of Ch2(Cy3) = INPUT
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
CHR04FS008303993 0.068683072999999 8.247565641 8.178882568 0 0.727387421
CHR03FS002757157 1.001326919 7.84672316 6.845396241 0 0.723756434
CHR05FS026930706 -0.770077142 9.108487827 9.878564969 0 0.84837861
CHR02FS001796874 -0.49943987 10.72260049 11.22204036 0 0.212756045
CHR03FS016996337 2.450394555 10.60571573 8.155321175 1 0.007569015
CHR05FS013588805 -0.869246733999999 8.178291285 9.047538019 0 0.999971031
CHR03FS005264720 3.87114265 14.13194428 10.26080163 1 1.30E-09
CHR05FS000610725 4.152899381 13.15918548 9.006286099 1 3.31E-07
CHR04FS015154295 -1.35544958 10.42944249 11.78489207 0 0.541629474
CHR05FS012579769 -1.752118403 7.935344505 9.687462908 0 0.999971031
CHR05FS008126778 2.61954016 13.85592956 11.2363894 1 1.07E-07
CHR01FS015810805 0.439609470000001 11.69829915 11.25868968 0 0.033356957
CHR03FS007739044 4.49543631 14.75195557 10.25651926 1 8.31E-12
CHR05FS015251447 -1.301524352 9.862770218 11.16429457 0 0.79890969
CHR01FS020044703 3.990305869 13.02087102 9.030565151 1 4.09E-08
CHR03FS009756975 0.497811332000001 9.967566891 9.469755559 0 0.2117756
CHR03FS007909494 -0.271429466 7.774445506 8.045874972 0 0.986708467
CHR05FS014006071 1.598397085 9.66930531 8.070908225 0 0.132504348
CHR03FS016398708 -2.234833875 7.889900585 10.12473446 0 0.999975968
CHR01FS007759128 -0.575367900999999 7.727081292 8.302449193 0 0.987270301

Total number of rows: 360718

Table truncated, full table size 23747 Kbytes.




Supplementary file Size Download File type/resource
GSM615057_12001402ColCvi_532.pair.gz 6.2 Mb (ftp)(http) PAIR
GSM615057_12001402ColCvi_635.pair.gz 5.9 Mb (ftp)(http) PAIR
Processed data included within Sample table

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