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Sample GSM151665 Query DataSets for GSM151665
Status Public on Dec 25, 2006
Title Root Vs. Embryo BP2
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 GPL1774
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 0.302199 265 239 602 401
26 -0.167175 280 256 524 374
51 0.238752 305 264 618 418
76 0.241563 354 251 640 375
101 0.551667 314 252 634 372
126 0.961283 275 241 634 361
151 0.379501 299 250 585 366
176 0.528509 261 234 632 410
201 0.394751 316 229 630 359
226 null 247 250 597 357
251 0.341799 401 251 690 351
276 -0.196668 263 238 502 351
301 -0.849448 283 238 482 357
326 -0.202162 924 245 1000 351
351 -0.190222 247 242 512 375
376 1.50238 234 231 642 372
401 0.549307 259 232 568 344
426 0.350664 270 247 548 346
451 0.0880526 288 239 531 341
476 0.404753 301 261 560 345

Total number of rows: 30000

Table truncated, full table size 916 Kbytes.




Supplementary file Size Download File type/resource
GSM151665.gpr.gz 1.9 Mb (ftp)(http) GPR

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