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Sample GSM569295 Query DataSets for GSM569295
Status Public on Jul 24, 2010
Title p4_10s027_MES_20090220_genepix6.gpr
Sample type RNA
 
Channel 1
Source name Julidochromis transcriptus female-JT22f
Organism Julidochromis transcriptus
Characteristics sex: female
species: Julidochromis transcriptus
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 transcriptus male-JT18m
Organism Julidochromis transcriptus
Characteristics sex: male
species: Julidochromis transcriptus
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_550 ScanPower=100_100
Description Cy3= Julidochromis transcriptus female aRNA Cy5= Julidochromis transcriptus 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 181 422 643 66 81 59 185 2419 8121 103 107 36 -100 null
hh_Ab_Pinky2003_000010108 335 494 442 69 87 67 266 439 363 104 114 47 -100 null
hh_Ab_Pinky2003_000010126 130 222 198 63 75 47 209 262 163 105 109 34 -100 null
hh_Ab_Pinky2003_000010132 349 582 593 61 73 41 423 545 408 104 103 28 -100 null
hh_Ab_Pinky2003_000010150 362 682 938 77 87 64 435 570 477 99 108 36 -100 null
hh_Ab_Pinky2003_000010156 228 305 282 66 74 42 171 244 165 103 105 26 -100 null
hh_Ab_Pinky2003_000010174 228 300 213 62 68 32 278 312 172 106 109 28 -100 null
hh_Ab_Pinky2003_000010180 175 319 388 62 72 46 187 329 333 105 110 45 -100 null
hh_Ab_Pinky2003_000010486 264 258 81 59 65 32 291 319 138 98 101 29 -100 null
hh_Ab_Pinky2003_000010492 151 258 335 62 70 39 199 295 312 101 104 31 0 -0.22
hh_Ab_Pinky2003_000010510 145 279 253 61 70 43 201 324 265 103 104 25 -100 null
hh_Ab_Pinky2003_000010516 116 185 203 66 75 50 146 197 141 105 109 35 0 null
hh_Ab_Pinky2003_000010534 204 232 144 65 73 37 191 235 127 105 107 27 -100 null
hh_Ab_Pinky2003_000010540 69 72 31 65 77 72 106 107 26 102 106 36 -50 null
hh_Ab_Pinky2003_000010558 355 461 334 69 76 41 348 405 255 102 105 30 0 0.03
hh_Ab_Pinky2003_000010564 250 267 129 74 79 43 200 211 62 107 111 43 -100 null
hh_Ab_Pinky2003_000010870 481 491 186 67 76 49 448 470 138 102 104 28 -100 null
hh_Ab_Pinky2003_000010876 106 173 167 67 73 48 133 181 123 98 101 27 -100 null
hh_Ab_Pinky2003_000010894 294 434 378 65 76 49 223 312 209 97 102 26 -100 null
hh_Ab_Pinky2003_000010900 228 424 475 69 77 41 267 461 497 100 102 26 -100 null

Total number of rows: 16894

Table truncated, full table size 1312 Kbytes.




Supplementary file Size Download File type/resource
GSM569295_p4_10s027_MES_20090220_genepix6.gpr.gz 1.7 Mb (ftp)(http) GPR
Processed data included within Sample table

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