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Sample GSM569308 Query DataSets for GSM569308
Status Public on Jul 24, 2010
Title p4_10s048_MES_20090328.gpr
Sample type RNA
 
Channel 1
Source name Julidochromis marlieri male-JMK64m
Organism Julidochromis marlieri
Characteristics sex: male
species: Julidochromis marlieri
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 marlieri female-JMK13f
Organism Julidochromis marlieri
Characteristics sex: female
species: Julidochromis marlieri
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=750_560 ScanPower=100_100
Description Cy3= Julidochromis marlieri male aRNA Cy5= Julidochromis marlieri 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 689 734 458 94 107 73 570 624 315 158 162 50 -100 null
hh_Ab_Pinky2003_000010108 1344 1557 930 120 164 185 1313 1441 703 167 196 132 -100 null
hh_Ab_Pinky2003_000010126 356 400 301 104 118 76 317 405 271 160 166 51 -100 null
hh_Ab_Pinky2003_000010132 593 744 595 88 104 65 596 914 701 157 161 45 -100 null
hh_Ab_Pinky2003_000010150 188 245 232 91 108 79 205 271 172 153 155 50 -100 null
hh_Ab_Pinky2003_000010156 631 702 454 95 108 64 537 591 305 152 156 36 -100 null
hh_Ab_Pinky2003_000010174 354 502 342 82 97 56 488 450 202 154 155 35 -100 null
hh_Ab_Pinky2003_000010180 240 561 693 82 97 58 235 452 443 147 150 37 -100 null
hh_Ab_Pinky2003_000010486 417 554 474 93 105 57 356 442 258 154 155 33 -100 null
hh_Ab_Pinky2003_000010492 733 1079 1067 93 107 70 501 897 857 158 163 49 -100 null
hh_Ab_Pinky2003_000010510 484 613 476 96 105 59 521 701 453 160 170 50 -100 null
hh_Ab_Pinky2003_000010516 360 436 293 102 125 76 416 407 190 150 160 54 -100 null
hh_Ab_Pinky2003_000010534 243 279 175 107 119 71 253 271 80 154 159 41 -100 null
hh_Ab_Pinky2003_000010540 269 510 528 96 108 68 484 508 265 140 139 35 -100 null
hh_Ab_Pinky2003_000010558 378 535 506 104 121 82 232 384 344 135 139 41 -100 null
hh_Ab_Pinky2003_000010564 389 468 327 135 157 104 361 447 276 155 167 64 -100 null
hh_Ab_Pinky2003_000010870 595 786 675 110 128 85 439 568 425 138 148 51 -100 null
hh_Ab_Pinky2003_000010876 198 390 506 111 166 293 215 377 427 140 181 255 -100 null
hh_Ab_Pinky2003_000010894 272 666 975 111 140 215 312 594 678 137 152 189 -100 null
hh_Ab_Pinky2003_000010900 531 814 791 102 117 69 496 863 857 134 138 44 -100 null

Total number of rows: 16894

Table truncated, full table size 1374 Kbytes.




Supplementary file Size Download File type/resource
GSM569308_p4_10s048_MES_20090328.gpr.gz 1.8 Mb (ftp)(http) GPR
Processed data included within Sample table

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