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Sample GSM569290 Query DataSets for GSM569290
Status Public on Jul 24, 2010
Title p4_10s009_MES_20090228_genepix6.gpr
Sample type RNA
 
Channel 1
Source name Julidochromis transcriptus female-JT21f
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 Cy3
Label protocol Message Amp II with single round amplification
 
Channel 2
Source name Julidochromis transcriptus male-JT14m
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 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=770_590 ScanPower=100_100
Description Cy3= Julidochromis transcriptus female aRNA Cy5= Julidochromis transcriptus male 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 195 417 638 104 120 76 356 498 388 207 219 84 -100 null
hh_Ab_Pinky2003_000010108 305 464 507 110 177 259 414 602 430 216 264 204 -100 null
hh_Ab_Pinky2003_000010126 267 447 446 110 167 208 361 493 340 222 268 203 -100 null
hh_Ab_Pinky2003_000010132 217 427 588 106 137 129 327 485 405 218 234 102 -100 null
hh_Ab_Pinky2003_000010150 268 510 510 100 123 98 420 648 528 210 220 82 -100 null
hh_Ab_Pinky2003_000010156 263 535 651 103 124 97 396 617 494 213 225 113 -100 null
hh_Ab_Pinky2003_000010174 269 517 611 106 121 86 331 488 413 212 222 111 -100 null
hh_Ab_Pinky2003_000010180 268 588 890 116 137 103 338 473 358 222 238 110 -100 null
hh_Ab_Pinky2003_000010486 711 1009 959 134 140 85 595 803 613 212 236 125 -100 null
hh_Ab_Pinky2003_000010492 188 368 467 112 141 143 300 438 349 205 224 133 -100 null
hh_Ab_Pinky2003_000010510 132 215 240 131 226 387 260 263 99 225 286 258 -100 null
hh_Ab_Pinky2003_000010516 285 645 872 114 154 223 413 639 505 208 230 162 -100 null
hh_Ab_Pinky2003_000010534 716 790 414 108 140 104 855 848 445 214 215 61 -100 null
hh_Ab_Pinky2003_000010540 1227 1555 1100 103 124 86 992 1137 627 219 219 64 -100 null
hh_Ab_Pinky2003_000010558 443 726 794 109 149 199 594 688 420 208 233 149 -100 null
hh_Ab_Pinky2003_000010564 200 383 477 119 207 323 342 424 272 219 291 257 -100 null
hh_Ab_Pinky2003_000010870 463 563 429 106 119 81 578 618 259 204 207 55 -100 null
hh_Ab_Pinky2003_000010876 190 360 445 107 131 127 297 409 288 207 220 81 -100 null
hh_Ab_Pinky2003_000010894 289 448 444 103 120 102 369 481 369 203 212 74 -100 null
hh_Ab_Pinky2003_000010900 243 412 489 103 133 146 299 420 308 202 221 113 -100 null

Total number of rows: 16894

Table truncated, full table size 1367 Kbytes.




Supplementary file Size Download File type/resource
GSM569290_p4_10s009_MES_20090228_genepix6.gpr.gz 1.8 Mb (ftp)(http) GPR
Processed data included within Sample table

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