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Sample GSM194558 Query DataSets for GSM194558
Status Public on Jun 30, 2008
Title TMK4_vip3_II
Sample type genomic
 
Source name 14 day old seedlings
Organism Arabidopsis thaliana
Characteristics Enriched for DNA associated with trimethylation of H3 K4
Aerial parts of 14 day old seedlings
Treatment protocol Untreated
Growth protocol Plants were grown under 16h light on soil
Extracted molecule genomic DNA
Extraction protocol Chromatin immunoprecipitation using anti-trimethylation of H3 K4 antibody (Upstate)
Label biotin
Label protocol Biotinylated DNA was prepared according to the Affymetrix® Chromatin Immunoprecipitation Assay Protocol (P/N 702238 Rev. 2, Affymetrix).
 
Hybridization protocol Following fragmentation, DNA was hybridized for 16 hr on GeneChip Arabidopsis Tiling 1.0R Array. GeneChips were washed and stained in the Affymetrix Fluidics Station according to the standard Affymetrix protocol.
Scan protocol GeneChips were scanned using The GeneChip Scanner 3000 7G
Description Enriched for DNA associated with trimethylation of H3 K4
Data processing Quantile Normalization using TileMap package
 
Submission date May 25, 2007
Last update date Dec 21, 2007
Contact name Sookyung Oh
E-mail(s) ohsookyu@msu.edu
Phone 517-355-5191-369
Organization name Michigan State University
Department Horticulture
Lab Steve van Nocker
Street address
City East Lansing
State/province MI
ZIP/Postal code 48824
Country USA
 
Platform ID GPL1979
Series (1)
GSE7907 Histone H3 modifications ChIP on chip

Data table header descriptions
ID_REF unique id constructed from x-y coordinates, chromosome, and start position
VALUE log2(quantile normalized probe-level PM-MM signal); "-1" results from PerfectMatch-MissMatch where MM is greater than PM

Data table
ID_REF VALUE
x1086_y1242_r2_Tag_2 -1
x1086_y1241_r2_Tag_10 -1
x1098_y1234_r2_Tag_22 -1
x1086_y1231_r2_Tag_28 4.011
x1088_y1237_r2_Tag_34 4.783
x1098_y1233_r2_Tag_36 1.16
x1088_y1236_r2_Tag_40 -1
x1102_y1246_r2_Tag_47 6.497
x1090_y1243_r2_Tag_51 6.967
x1084_y1246_r2_Tag_65 6.237
x1090_y1242_r2_Tag_67 6.497
x1084_y1245_r2_Tag_69 -1
x1098_y1232_r2_Tag_79 3.35
x1090_y1241_r2_Tag_85 -1
x1102_y1245_r2_Tag_94 -1
x1088_y1247_r2_Tag_96 3.35
x1090_y1240_r2_Tag_104 -1
x1090_y1238_r2_Tag_111 5.81
x1084_y1244_r2_Tag_114 2.745
x1100_y1247_r2_Tag_118 6.12

Total number of rows: 3080567

Table truncated, full table size 90306 Kbytes.




Supplementary file Size Download File type/resource
GSM194558.CEL.gz 26.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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