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Sample GSM310840 Query DataSets for GSM310840
Status Public on Sep 11, 2008
Title ChIP_H3K9me2_crosslinked_rep1
Sample type genomic
 
Channel 1
Source name ChIP crosslinked H3K9me2
Organism Arabidopsis thaliana
Characteristics Col-0, 3 week old, aerial part of the plant
Treatment protocol Aerial part of the plants were crosslinked in 1% formaldehyde for 15 minutes. Crosslinking was stopped with addition of glycine to 0.125 M final concentration and plants were frozen in the liquid nitrogen.
Growth protocol Plants were grown under continuous light for three weeks.
Extracted molecule genomic DNA
Extraction protocol ChIP was performed as described:
Gendrel AV, Lippman Z, Yordan C, Colot V, Martienssen RA (2002)
Dependence of heterochromatic histone H3 methylation patterns on the
Arabidopsis gene DDM1. Science 297: 1871–1873.
Mouse monoclonal antibody anti-H3K9me2 (Abcam #ab1220; http://www.abcam.com) was used for immunoprecipitation.
Label Cy5
Label protocol According to standard NimbleGen protocols (www.nimblegen.com)
 
Channel 2
Source name ChIP crosslinked H3
Organism Arabidopsis thaliana
Characteristics Col-0, 3 week old, aerial part of the plant
Treatment protocol Aerial part of the plants were crosslinked in 1% formaldehyde for 15 minutes. Crosslinking was stopped with addition of glycine to 0.125 M final concentration and plants were frozen in the liquid nitrogen.
Growth protocol Plants were grown under continuous light for three weeks.
Extracted molecule genomic DNA
Extraction protocol ChIP was performed as described:
Gendrel AV, Lippman Z, Yordan C, Colot V, Martienssen RA (2002)
Dependence of heterochromatic histone H3 methylation patterns on the
Arabidopsis gene DDM1. Science 297: 1871–1873.
Rabbit polyclonal antibody anti-H3 (Abcam #ab1791; http://www.abcam.com) was used for immunoprecipitation.
Label Cy3
Label protocol According to standard NimbleGen protocols (www.nimblegen.com)
 
 
Hybridization protocol According to standard NimbleGen protocols (www.nimblegen.com)
Scan protocol According to standard NimbleGen protocols (www.nimblegen.com)
Description no additional information
Data processing Each probe was assigned a log of the ratio between H3K9me2 (Cy5) and H3 (Cy3) signal. Z-scores were calculated for each probe by subtracting the mean log ratio from individual log ratios and dividing by the standard deviation for the entire array.
 
Submission date Aug 07, 2008
Last update date Sep 11, 2008
Contact name Steve E Jacobsen
E-mail(s) yaniki@ucla.edu
Phone (310) 825-0182
URL http://www.mcdb.ucla.edu/Research/Jacobsen/index.html
Organization name University of California, Los Angeles
Department Molecular Cell and Developmental Biology
Lab Jacobsen lab
Street address 621 Charles E. Young Dr. South
City Los Angeles
State/province CA
ZIP/Postal code 90095-1606
Country USA
 
Platform ID GPL7143
Series (1)
GSE12383 Genome wide profiling of H3K9me2 in Arabidopsis thaliana

Data table header descriptions
ID_REF
VALUE log e (Cy5/Cy3)ratio-mean)/standard deviation

Data table
ID_REF VALUE
CHR1V01212004FS000000001 1.571054
CHR1V01212004FS000000061 0.771189
CHR1V01212004FS000000121 0.817496
CHR1V01212004FS000000181 0.317298
CHR1V01212004FS000000241 0.256085
CHR1V01212004FS000000301 0.253072
CHR1V01212004FS000000361 -0.193763
CHR1V01212004FS000000421 0.195189
CHR1V01212004FS000000481 0.059756
CHR1V01212004FS000000541 0.000068
CHR1V01212004FS000000601 0.002316
CHR1V01212004FS000000661 0.048621
CHR1V01212004FS000000721 0.087837
CHR1V01212004FS000000781 0.122054
CHR1V01212004FS000000841 -0.298301
CHR1V01212004FS000000901 -0.184169
CHR1V01212004FS000000961 0.564201
CHR1V01212004FS000001021 0.215696
CHR1V01212004FS000001081 0.819623
CHR1V01212004FS000001141 0.282279

Total number of rows: 2001685

Table truncated, full table size 67590 Kbytes.




Supplementary file Size Download File type/resource
GSM310840_Cy5_Cy3.txt.gz 18.6 Mb (ftp)(http) TXT
Processed data included within Sample table

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