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Sample GSM151642 Query DataSets for GSM151642
Status Public on Dec 25, 2006
Title Embryo vs. Callus AP2
Sample type RNA
 
Channel 1
Source name Callus (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 Embryo (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 somatic embryos.
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 -0.862057 370 204 298 186
26 -2.40159 260 197 207 177
51 0.0714914 506 217 462 199
76 -0.551842 334 257 331 235
101 0.670101 1009 294 1061 253
126 0.0556778 846 329 653 269
151 -1.452 405 292 319 253
176 -1.05358 364 277 317 242
201 0.130496 3024 286 2082 266
226 -0.343674 334 288 338 250
251 0.192163 778 299 654 254
276 0.170527 3613 278 2467 236
301 0.572451 515 235 564 209
326 -2.20958 292 249 256 227
351 -0.213754 2307 248 1325 238
376 0.595275 723 238 782 232
401 0.35445 331 253 399 233
426 0.175004 583 242 527 221
451 0.480314 884 243 867 234
476 0.198872 1058 237 854 226

Total number of rows: 30000

Table truncated, full table size 930 Kbytes.




Supplementary file Size Download File type/resource
GSM151642.gpr.gz 2.1 Mb (ftp)(http) GPR

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