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Sample GSM569309 Query DataSets for GSM569309
Status Public on Jul 24, 2010
Title p4_10s049_MES_20090328.gpr
Sample type RNA
 
Channel 1
Source name Julidochromis marlieri female-JMK53f
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 Cy3
Label protocol Message Amp II with single round amplification
 
Channel 2
Source name Julidochromis marlieri male-JMK48m
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 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=730_590 ScanPower=100_100
Description Cy3= Julidochromis marlieri female aRNA Cy5= Julidochromis marlieri 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 718 1771 3308 52 60 34 1438 5850 9513 61 65 27 -100 null
hh_Ab_Pinky2003_000010108 332 816 1038 76 197 1502 434 898 995 182 599 4507 -100 null
hh_Ab_Pinky2003_000010126 239 280 184 75 88 58 367 448 278 193 198 66 -100 null
hh_Ab_Pinky2003_000010132 689 1020 1037 78 103 124 928 5295 8491 191 214 133 -100 null
hh_Ab_Pinky2003_000010150 377 464 308 85 91 46 807 766 315 175 186 62 -100 null
hh_Ab_Pinky2003_000010156 392 575 495 78 93 101 549 1305 2551 173 211 369 -100 null
hh_Ab_Pinky2003_000010174 98 148 191 82 1652 9381 174 228 179 179 2017 10051 -100 null
hh_Ab_Pinky2003_000010180 208 627 1939 86 696 5180 403 1785 7154 184 1277 7123 -100 null
hh_Ab_Pinky2003_000010486 770 782 347 75 88 48 1225 1194 461 174 185 79 -100 null
hh_Ab_Pinky2003_000010492 342 707 819 84 97 89 545 838 748 189 204 122 -100 null
hh_Ab_Pinky2003_000010510 249 480 516 96 162 398 419 716 582 188 611 2425 -100 null
hh_Ab_Pinky2003_000010516 401 516 372 96 104 59 549 861 682 177 185 58 -100 null
hh_Ab_Pinky2003_000010534 441 447 184 79 90 53 542 657 350 166 178 58 -100 null
hh_Ab_Pinky2003_000010540 867 990 624 75 90 48 1223 1304 885 156 162 44 -100 null
hh_Ab_Pinky2003_000010558 635 723 516 87 100 63 955 1005 686 172 185 68 -100 null
hh_Ab_Pinky2003_000010564 297 346 262 86 96 63 455 637 458 169 179 67 -100 null
hh_Ab_Pinky2003_000010870 1132 1161 602 80 93 56 1114 1246 550 162 165 50 -100 null
hh_Ab_Pinky2003_000010876 168 326 436 85 99 62 249 443 527 166 172 53 -100 null
hh_Ab_Pinky2003_000010894 256 531 764 86 98 57 255 547 761 158 165 54 -100 null
hh_Ab_Pinky2003_000010900 1052 1904 1918 88 100 72 1311 2092 2114 160 171 88 -100 null

Total number of rows: 16894

Table truncated, full table size 1364 Kbytes.




Supplementary file Size Download File type/resource
GSM569309_p4_10s049_MES_20090328.gpr.gz 1.8 Mb (ftp)(http) GPR
Processed data included within Sample table

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