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Sample GSM569292 Query DataSets for GSM569292
Status Public on Jul 24, 2010
Title p4_10s013_MES_20090312_genepix 6.gpr
Sample type RNA
 
Channel 1
Source name Julidochromis transcriptus male-JT15m
Organism Julidochromis transcriptus
Characteristics sex: male
species: Julidochromis transcriptus
Biomaterial provider Renn lab
Treatment protocol none
Growth protocol Fish were grown in 30 gallon stock tanks under standard lab conditions
Extracted molecule total RNA
Extraction protocol Trizol extraction
Label Cy3
Label protocol Message Amp II with single round amplification
 
Channel 2
Source name Julidochromis transcriptus female-JT20f
Organism Julidochromis transcriptus
Characteristics sex: female
species: Julidochromis transcriptus
Biomaterial provider Renn lab
Treatment protocol none
Growth protocol Fish were grown in 30 gallon stock tanks under standard lab conditions
Extracted molecule total RNA
Extraction protocol Trizol extraction
Label Cy5
Label protocol Message Amp II with single round amplification
 
 
Hybridization protocol The samples were combined with hybridization buffer (Ambion Slide hybe buffer #1) and hybridized to the microarray at 48 degrees 16-24 hours
Scan protocol Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0.
PMTGain=810_620 ScanPower=100_100
Description Cy3= Julidochromis transcriptus male aRNA Cy5= Julidochromis transcriptus female aRNA
Data processing After removing ""flagged"" and bad spots, only those spots were used whose average intensity was at least two standard deviations above the average background. Arrays were background corrected (method minimal) and normalized LIMMA in R/Bioconductor using within-arrays print-tip-loess normaliztion, intensity ratios were estimated and p-values calculated using the exact method adapted from the lmFit and EBayes commands.
 
Submission date Jul 22, 2010
Last update date Jul 23, 2010
Contact name Suzy C.P. Renn
E-mail(s) renns@reed.edu
Phone 503 517 7967
Organization name Reed College
Department Biology
Street address 3203 SE Woodstock Blvd
City Portland
State/province OR
ZIP/Postal code 97202
Country USA
 
Platform ID GPL6416
Series (1)
GSE23094 Julidochromis species male vs. female 20100721

Data table header descriptions
ID_REF Unique ID of feature located at "Block", "Column", "Row": redundant with platform file for most
F635 Median 635nm Foreground intensity Median
F635 Mean 635nm Foreground intensity Mean
F635 SD 635nm Foreground intensity Standard Deviation
B635 Median 635nm Background intensity Median
B635 Mean 635nm Background intensity Mean
B635 SD 635nm Background intensity Standard Deviation
F532 Median 532nm Foreground intensity Median
F532 Mean 532nm Foreground intensity Mean
F532 SD 532nm Foreground intensity Standard Deviation
B532 Median 532nm Background intensity Median
B532 Mean 532nm Background intensity Mean
B532 SD 532nm Background intensity Standard Deviation
Flags Feature Flags: both automated and mannually applied
VALUE log2 Cy5/Cy3 ratio normalized within arrays using loess after background subtraction and quality filtering

Data table
ID_REF F635 Median F635 Mean F635 SD B635 Median B635 Mean B635 SD F532 Median F532 Mean F532 SD B532 Median B532 Mean B532 SD Flags VALUE
hh_Ab_Pinky2003_000010102 1505 1762 1300 257 352 348 2085 2072 1189 301 346 248 -100 null
hh_Ab_Pinky2003_000010108 477 1022 1324 212 289 290 644 1144 1170 273 300 136 -100 null
hh_Ab_Pinky2003_000010126 1238 1754 1413 252 385 548 1384 1552 1206 293 365 337 -100 null
hh_Ab_Pinky2003_000010132 945 1868 2029 197 276 372 962 1410 1188 272 329 266 -100 null
hh_Ab_Pinky2003_000010150 1280 2377 2077 176 218 157 1158 1525 1128 242 254 85 -100 null
hh_Ab_Pinky2003_000010156 1743 2094 1704 170 228 262 1459 1546 720 230 267 257 -100 null
hh_Ab_Pinky2003_000010174 701 1485 1973 154 192 161 646 1273 2395 224 243 174 -100 null
hh_Ab_Pinky2003_000010180 428 843 1073 162 209 164 440 767 710 224 241 102 -100 null
hh_Ab_Pinky2003_000010486 596 1588 2383 163 216 230 428 1048 1292 225 261 149 -100 null
hh_Ab_Pinky2003_000010492 535 1126 1408 162 203 187 519 974 965 223 242 109 -100 null
hh_Ab_Pinky2003_000010510 1268 2057 1844 176 222 194 1421 1638 973 243 260 113 -100 null
hh_Ab_Pinky2003_000010516 349 849 1116 140 171 137 452 730 638 219 227 84 -100 null
hh_Ab_Pinky2003_000010534 275 860 1372 134 161 133 291 706 990 209 217 70 -100 null
hh_Ab_Pinky2003_000010540 488 878 964 139 173 160 576 961 969 209 219 76 -100 null
hh_Ab_Pinky2003_000010558 609 1024 1217 138 167 147 675 995 1006 210 220 85 -100 null
hh_Ab_Pinky2003_000010564 2252 2791 2033 199 225 180 1028 1643 1429 254 268 126 -100 null
hh_Ab_Pinky2003_000010870 1077 1258 891 133 169 127 1108 1169 534 208 217 91 -100 null
hh_Ab_Pinky2003_000010876 523 813 824 144 185 195 581 790 576 209 224 111 -100 null
hh_Ab_Pinky2003_000010894 472 1308 1677 153 240 444 491 1081 1214 224 271 269 -100 null
hh_Ab_Pinky2003_000010900 408 828 1072 150 255 472 454 733 706 218 285 328 -100 null

Total number of rows: 16894

Table truncated, full table size 1370 Kbytes.




Supplementary file Size Download File type/resource
GSM569292_p4_10s013_MES_20090312_genepix_6.gpr.gz 1.8 Mb (ftp)(http) GPR
Processed data included within Sample table

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