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Sample GSM569304 Query DataSets for GSM569304
Status Public on Jul 24, 2010
Title p4_10s021_MES_20090215_genepix6.gpr
Sample type RNA
 
Channel 1
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 Cy3
Label protocol Message Amp II with single round amplification
 
Channel 2
Source name Julidochromis marlieri female-JMK35f
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=800_490 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 197 237 110 111 123 82 281 291 81 91 94 23 -100 null
hh_Ab_Pinky2003_000010108 242 286 229 94 116 78 213 321 276 84 89 30 -100 null
hh_Ab_Pinky2003_000010126 200 193 108 107 125 87 132 141 43 80 81 16 -100 null
hh_Ab_Pinky2003_000010132 107 122 78 110 123 75 85 89 26 80 81 14 -50 null
hh_Ab_Pinky2003_000010150 106 119 74 102 115 73 83 92 34 80 81 15 -50 null
hh_Ab_Pinky2003_000010156 219 248 189 109 127 82 222 237 84 81 84 18 -100 null
hh_Ab_Pinky2003_000010174 109 130 81 108 122 85 80 81 13 80 81 17 -50 null
hh_Ab_Pinky2003_000010180 277 317 183 104 129 89 231 249 122 86 89 23 0 0.3
hh_Ab_Pinky2003_000010486 141 163 111 105 128 83 99 117 47 81 86 23 -100 null
hh_Ab_Pinky2003_000010492 418 410 264 132 143 87 320 325 202 92 94 20 -100 null
hh_Ab_Pinky2003_000010510 133 141 81 113 130 80 92 95 27 90 91 16 -50 null
hh_Ab_Pinky2003_000010516 112 123 84 119 132 80 95 97 18 93 96 21 -50 null
hh_Ab_Pinky2003_000010534 120 139 88 110 128 81 101 115 45 92 94 19 -50 null
hh_Ab_Pinky2003_000010540 107 149 98 96 116 89 142 159 49 92 90 18 -100 null
hh_Ab_Pinky2003_000010558 378 394 217 132 160 112 360 346 110 97 108 56 -100 null
hh_Ab_Pinky2003_000010564 223 262 150 126 134 72 133 137 41 87 88 19 -100 null
hh_Ab_Pinky2003_000010870 247 268 132 106 124 78 207 217 64 85 86 15 0 0.27
hh_Ab_Pinky2003_000010876 131 144 87 113 167 523 84 85 20 86 133 670 -50 null
hh_Ab_Pinky2003_000010894 561 606 431 136 209 610 708 730 479 96 178 790 0 null
hh_Ab_Pinky2003_000010900 220 318 338 128 147 101 210 410 497 91 99 47 0 null

Total number of rows: 16894

Table truncated, full table size 1304 Kbytes.




Supplementary file Size Download File type/resource
GSM569304_p4_10s021_MES_20090215_genepix6.gpr.gz 1.7 Mb (ftp)(http) GPR
Processed data included within Sample table

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