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Sample GSM151645 Query DataSets for GSM151645
Status Public on Dec 25, 2006
Title Shoot 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 Shoot (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 shoots.
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 -0.208085 239 212 236 199
26 -0.810829 256 224 237 208
51 -0.434531 1855 237 1438 216
76 -0.570743 414 221 359 217
101 0.684284 360 234 447 219
126 0.236271 305 245 312 228
151 -1.12466 249 238 244 231
176 -0.0982285 811 234 803 227
201 0.294919 625 240 742 229
226 0.129219 240 232 252 230
251 -2.10533 297 229 260 238
276 0.117488 1159 235 1283 245
301 null 235 249 242 245
326 0.815219 279 248 308 232
351 0.205602 465 240 505 223
376 0.4875 320 231 372 234
401 null 208 239 250 238
426 -0.211904 353 240 344 238
451 0.311594 380 240 415 221
476 0.0511657 494 240 510 225

Total number of rows: 30000

Table truncated, full table size 900 Kbytes.




Supplementary file Size Download File type/resource
GSM151645.gpr.gz 1.9 Mb (ftp)(http) GPR

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