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Sample GSM114747 Query DataSets for GSM114747
Status Public on Aug 30, 2006
Title XZ_tripleWhole_mCIPUB_02_F0130_07022005.CEL
Sample type genomic
 
Source name whole palnt tissue w/o root, 40 days
Organism Arabidopsis thaliana
Characteristics Depleted for methylated DNA at all sequenced contexts
Treatment protocol Untreated
Growth protocol Plants were grown on soil under continuous illumination for 40 days at 25 degrees C
Extracted molecule genomic DNA
Extraction protocol genomic DNA was isolated from whole plant tissues using DNAeasy kit following instructions from the manufacturer (QIAGEN) instruction
Label biotin
Label protocol The genomic DNA in the samples was 3'-end-labelled with dd-UTP (Roche) by the terminal transferase (TdT, Roche) reaction for 1 h at 37 degrees C.
 
Hybridization protocol Whole Genome Tiling Array was hybridized for 16 hrs, washed and stained with a streptavidin-phycoerythrin conjugate on the Affymetrix Fluidics Station 400 according to the standard Affymetrix protocol.
Scan protocol GeneChips were scanned on Affymetrix scanner G7
Description Depleted for methylated DNA at all sequenced contexts
Data processing Gene chip data files were processed using TileMap and KS method.
 
Submission date Jun 15, 2006
Last update date Aug 25, 2006
Contact name Steve E Jacobsen
E-mail(s) [email protected]
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 GPL1979
Series (1)
GSE5094 High Resolution Mapping and Functional Analysis of the Methylome in Arabidopsis (mCIP, MBD)

Data table header descriptions
ID_REF unique id constructed from x-y coordinates, chromosome, and start position
VALUE signal is calculated DNA abundance using TileMap software and KS method.

Data table
ID_REF VALUE
x5_y1_chr3_10175144 264.0
x7_y1_gcBin12_1 87.0
x9_y1_chr1_645437 95.0
x11_y1_chr2_9163417 90.0
x13_y1_gcBin15_1 215.0
x15_y1_gcBin16_1 79.0
x17_y1_gcBin17_1 151.0
x19_y1_gcBin15_1 73.0
x21_y1_gcBin12_1 116.0
x23_y1_gcBin11_1 90.0
x25_y1_chr5_4588435 83.0
x27_y1_chr4_6511863 114.0
x29_y1_chr4_11490101 110.0
x31_y1_chr5_14020565 104.0
x33_y1_chr1_13157838 245.0
x35_y1_chr4_14849064 130.0
x37_y1_chr2_3757501 341.0
x39_y1_chr4_774577 88.0
x41_y1_chr1_7288319 315.0
x43_y1_chr1_22480092 85.0

Total number of rows: 3092374

Table truncated, full table size 91184 Kbytes.




Supplementary file Size Download File type/resource
GSM114747.CEL.gz 38.4 Mb (ftp)(http) CEL

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