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Sample GSM151647 Query DataSets for GSM151647
Status Public on Dec 25, 2006
Title Root Vs. Embryo AP2
Sample type RNA
 
Channel 1
Source name Embryo (reference)
Organism Oryza sativa
Characteristics indica rice cultivar 93-11
Extracted molecule total RNA
Extraction protocol Trizol/RNeasy
Label Cy5
Label protocol amino-allyl and monofunctional dye
 
Channel 2
Source name Root (experiment)
Organism Oryza sativa
Characteristics indica rice cultivar 93-11
Extracted molecule total RNA
Extraction protocol Trizol/RNeasy
Label Cy3
Label protocol amino-allyl and monofunctional dye
 
 
Hybridization protocol 42C 50% formamide
Scan protocol Axon GenePix 4000B
Description Identification of genes differentially expressed during formation of roots.
Data processing To identify and remove systematic sources of variation, spot intensities from the GenePix Pro output files of all repeats of a given sample pair were normalized using the limma package in R. The print-tip lowess normalization method was used.
 
Submission date Dec 17, 2006
Last update date Dec 20, 2006
Contact name Kun He
E-mail(s) hek@mail.cbi.pku.edu.cn
Phone 203-432-8909
Organization name Yale University
Department Molecular, Cellular & Developmental Biology
Lab Denglab
Street address 165 Prospect
City New Haven
State/province CT
ZIP/Postal code 06520
Country USA
 
Platform ID GPL1773
Series (1)
GSE6552 Transcriptome associates with rice organogenesis

Data table header descriptions
ID_REF
VALUE Normalized log2 ratio of (experiment_channel/reference_channel)
CH1_SIG_MEAN Channel 1 (635 nm, Cy5) mean pixel intensity
CH1_BKG_MEDIAN Channel 1 Background median
CH2_SIG_MEAN Channel 2 (532 nm, Cy3) mean pixel intensity
CH2_BKG_MEDIAN Channel 2 Background median

Data table
ID_REF VALUE CH1_SIG_MEAN CH1_BKG_MEDIAN CH2_SIG_MEAN CH2_BKG_MEDIAN
1 null 193 171 148 148
26 null 165 171 148 146
51 -3.30667 191 172 153 146
76 -0.788018 174 163 161 140
101 0.0279155 357 154 425 143
126 -0.0208037 186 171 180 138
151 -1.89162 218 180 171 143
176 -0.233884 600 167 564 138
201 -1.49861 171 167 140 133
226 -0.0743776 190 168 192 136
251 -2.77016 186 166 151 141
276 0.301594 558 174 678 140
301 -0.219437 205 182 192 139
326 -0.0377574 207 186 199 144
351 -0.0644548 462 201 478 157
376 -0.516479 248 204 249 165
401 1.09603 198 186 235 165
426 -0.730355 212 187 196 155
451 -0.695308 322 182 297 150
476 0.228137 389 176 473 144

Total number of rows: 30000

Table truncated, full table size 913 Kbytes.




Supplementary file Size Download File type/resource
GSM151647.gpr.gz 1.9 Mb (ftp)(http) GPR

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