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Sample GSM569301 Query DataSets for GSM569301
Status Public on Jul 24, 2010
Title p4_10s008_20090228_genepix6.gpr
Sample type RNA
 
Channel 1
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 Cy3
Label protocol Message Amp II with single round amplification
 
Channel 2
Source name Julidochromis marlieri male-JMK52m
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=710_550 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 157 280 325 71 81 41 253 378 304 124 130 42 -100 null
hh_Ab_Pinky2003_000010108 201 305 308 82 123 170 323 462 365 135 184 185 -100 null
hh_Ab_Pinky2003_000010126 191 258 206 80 98 68 310 404 266 137 162 101 -100 null
hh_Ab_Pinky2003_000010132 168 258 266 85 101 83 251 353 271 137 160 103 -100 null
hh_Ab_Pinky2003_000010150 122 180 164 74 85 47 187 290 267 126 135 56 -100 null
hh_Ab_Pinky2003_000010156 205 276 276 73 85 67 308 451 398 122 133 64 -100 null
hh_Ab_Pinky2003_000010174 224 355 320 74 84 47 397 521 400 126 136 65 -100 null
hh_Ab_Pinky2003_000010180 128 187 162 76 87 51 228 307 213 128 138 56 -100 null
hh_Ab_Pinky2003_000010486 178 491 659 75 87 64 268 514 460 120 135 65 -100 null
hh_Ab_Pinky2003_000010492 168 242 212 77 105 125 226 376 335 127 170 178 -100 null
hh_Ab_Pinky2003_000010510 116 196 207 75 87 58 168 358 412 123 131 51 -100 null
hh_Ab_Pinky2003_000010516 193 1419 5017 82 99 83 281 525 696 126 150 132 -100 null
hh_Ab_Pinky2003_000010534 182 310 318 81 97 83 320 498 416 129 158 135 -100 null
hh_Ab_Pinky2003_000010540 387 408 304 77 91 71 549 680 436 126 142 95 -100 null
hh_Ab_Pinky2003_000010558 277 371 303 76 94 83 457 574 458 124 148 129 0 -0.13
hh_Ab_Pinky2003_000010564 170 287 349 85 133 148 240 404 377 133 214 246 -50 null
hh_Ab_Pinky2003_000010870 235 316 290 74 85 56 372 441 246 122 130 52 0 0.06
hh_Ab_Pinky2003_000010876 312 377 267 96 118 115 646 607 239 131 162 109 -100 null
hh_Ab_Pinky2003_000010894 203 266 206 77 94 77 379 445 334 125 144 94 0 -0.3
hh_Ab_Pinky2003_000010900 185 240 201 78 91 67 271 362 252 126 139 82 0 null

Total number of rows: 16894

Table truncated, full table size 1310 Kbytes.




Supplementary file Size Download File type/resource
GSM569301_p4_10s008_20090228_genepix6.gpr.gz 1.7 Mb (ftp)(http) GPR
Processed data included within Sample table

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