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Sample GSM611110 Query DataSets for GSM611110
Status Public on May 17, 2011
Title 7355302 - Col vs Cvi
Sample type genomic
 
Channel 1
Source name Cvi
Organism Arabidopsis thaliana
Characteristics ecotype: cvi
age: 15day
developmental stage: seedling (Boyes et al. Plant Cell 2001)
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 Cvi:10ug. (DNeasy_Plant_Qiagen.pdf)
Label Cy5
Label protocol labelling Cy3 and Cy5 direct, amplification=no, DNA .
 
Channel 2
Source name Col
Organism Arabidopsis thaliana
Characteristics ecotype: col-0
age: 15day
developmental stage: seedling (Boyes et al. Plant Cell 2001)
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 Col:10ug. (DNeasy_Plant_Qiagen.pdf)
Label Cy3
Label protocol labelling Cy3 and Cy5 direct, amplification=no, DNA .
 
 
Hybridization protocol Cvi Cy5 / Col Cy3 : 120pmol. (Hyb_Scan_Nimb_GEO.doc)
Scan protocol NimbleGen, Cy3:pmt voltage 532nm,650V,laser power 100%, Cy5:635nm,pmt voltage 700V,laser power 100%
Description 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 Comparative Genome Hybridization datat were analyzed using hidden Markov models as described in Seifert, M., Banaei, A., Keilwagen, J., Mette, M.F., Houben, A., Roudier, F., Colot, V., Grosse, I. and Strickert, M. (2009) Array-based genome comparison of Arabidopsis ecotypes using hidden Markov models, Proceedings of Biosignals , Second International Conference on Bio-inspired Systems and Signal Processing, ISBN: 978-989-8111-65-4, p. 3-11.
 
Submission date Oct 20, 2010
Last update date May 17, 2011
Contact name Véronique BRUNAUD
E-mail(s) veronique.brunaud@inrae.fr
Organization name INRA - CNRS - UPSUD
Lab IPS2
Street address rue Noetzlin
City Gif-sur-Yvette
ZIP/Postal code 91190
Country France
 
Platform ID GPL10920
Series (2)
GSE24835 cgh_colvscvi_wg-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions
GSE24836 Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions

Data table header descriptions
ID_REF ID number
VALUE Normalized log2 ratio median intensity of Ch2(Cy3)/Ch1(Cy5) (Ch1=reference)
Pvalue Pvalue if status=1
Status 0/1 1 if significant differential signal and 0 otherwise

Data table
ID_REF VALUE Pvalue Status
CHR01FS000000061 -0.47041 . 0
CHR01FS000000382 0.21046 . 0
CHR01FS000000707 -0.76071 . 0
CHR01FS000001012 0.17149 . 0
CHR01FS000001382 0.46535 . 0
CHR01FS000001687 0.16359 . 0
CHR01FS000001982 0.07517 . 0
CHR01FS000002367 0.01158 . 0
CHR01FS000002672 -0.2158 . 0
CHR01FS000002972 -0.09125 . 0
CHR01FS000003349 0.37653 . 0
CHR01FS000003664 0.1685 . 0
CHR01FS000003986 0.1361 . 0
CHR01FS000004351 0.29786 . 0
CHR01FS000004681 0.29609 . 0
CHR01FS000004986 0.25759 . 0
CHR01FS000005311 0.14337 . 0
CHR01FS000005611 -0.04459 . 0
CHR01FS000005969 -0.22197 . 0
CHR01FS000006289 0.03368 . 0

Total number of rows: 360718

Table truncated, full table size 10506 Kbytes.




Supplementary file Size Download File type/resource
GSM611110_7355302_532.pair.gz 6.0 Mb (ftp)(http) PAIR
GSM611110_7355302_635.pair.gz 6.0 Mb (ftp)(http) PAIR
Processed data included within Sample table
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