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Sample GSM569306 Query DataSets for GSM569306
Status Public on Jul 24, 2010
Title p4_10s035_MES_20090326.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-JMK11f
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=700_570 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 223 301 238 103 156 244 320 508 402 183 242 294 -100 null
hh_Ab_Pinky2003_000010108 344 1133 1846 101 125 93 474 1323 1852 169 189 95 -100 null
hh_Ab_Pinky2003_000010126 429 917 977 89 158 465 500 1046 995 155 222 483 -100 null
hh_Ab_Pinky2003_000010132 149 161 80 92 224 796 306 353 223 167 288 594 -100 null
hh_Ab_Pinky2003_000010150 627 1370 1480 72 84 55 891 1471 1495 140 154 71 -100 null
hh_Ab_Pinky2003_000010156 1229 1550 1143 81 88 44 1450 1750 1333 133 150 94 -100 null
hh_Ab_Pinky2003_000010174 86 427 1038 75 84 44 142 561 1299 129 137 52 -100 null
hh_Ab_Pinky2003_000010180 223 708 1014 71 80 45 348 953 1421 126 140 59 -100 null
hh_Ab_Pinky2003_000010486 74 105 89 79 254 764 154 250 239 138 368 996 -100 null
hh_Ab_Pinky2003_000010492 182 628 1059 77 134 371 342 852 1305 134 230 634 -100 null
hh_Ab_Pinky2003_000010510 115 392 821 74 82 40 246 698 1069 136 147 70 -100 null
hh_Ab_Pinky2003_000010516 110 343 625 72 81 51 203 567 912 127 144 122 -100 null
hh_Ab_Pinky2003_000010534 126 352 538 74 104 214 410 596 643 129 151 115 -100 null
hh_Ab_Pinky2003_000010540 106 193 285 67 76 48 240 467 600 120 128 49 -100 null
hh_Ab_Pinky2003_000010558 159 753 1597 79 155 272 223 1147 2509 130 240 389 -100 null
hh_Ab_Pinky2003_000010564 172 453 674 75 86 53 290 671 855 122 140 96 -100 null
hh_Ab_Pinky2003_000010870 550 629 411 73 79 41 797 930 586 121 133 68 -100 null
hh_Ab_Pinky2003_000010876 163 425 564 72 84 91 237 640 870 119 130 57 -100 null
hh_Ab_Pinky2003_000010894 113 894 3078 71 79 69 255 1106 2417 121 127 44 -100 null
hh_Ab_Pinky2003_000010900 318 557 730 68 76 49 544 884 879 118 124 43 -100 null

Total number of rows: 16894

Table truncated, full table size 1402 Kbytes.




Supplementary file Size Download File type/resource
GSM569306_p4_10s035_MES_20090326.gpr.gz 1.9 Mb (ftp)(http) GPR
Processed data included within Sample table

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