NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM569293 Query DataSets for GSM569293
Status Public on Jul 24, 2010
Title p4_10s014_JBC_20090315_genepix6.gpr
Sample type RNA
 
Channel 1
Source name Julidochromis transcriptus female-JT29f
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-JT15m
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=760_520 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 852 1098 928 123 208 305 886 1074 790 108 207 336 -100 null
hh_Ab_Pinky2003_000010108 383 777 904 96 136 164 319 624 744 89 118 157 -100 null
hh_Ab_Pinky2003_000010126 283 474 431 103 172 317 201 435 420 91 147 211 -100 null
hh_Ab_Pinky2003_000010132 238 481 663 99 150 250 163 419 566 87 125 171 -100 null
hh_Ab_Pinky2003_000010150 240 510 603 94 114 85 198 474 572 86 96 51 -100 null
hh_Ab_Pinky2003_000010156 636 930 942 104 122 114 452 675 555 88 101 84 -100 null
hh_Ab_Pinky2003_000010174 275 791 1163 98 125 114 221 548 907 93 106 67 -100 null
hh_Ab_Pinky2003_000010180 364 1715 6414 98 123 99 273 1058 1873 96 115 90 -100 null
hh_Ab_Pinky2003_000010486 355 714 873 101 129 107 378 877 1159 90 103 60 -100 null
hh_Ab_Pinky2003_000010492 515 1158 1393 105 135 115 439 915 1076 91 107 66 -100 null
hh_Ab_Pinky2003_000010510 715 1363 1482 111 139 118 637 998 1354 96 110 55 -100 null
hh_Ab_Pinky2003_000010516 352 815 867 114 145 115 598 857 779 99 119 105 -100 null
hh_Ab_Pinky2003_000010534 316 935 1294 109 147 211 212 926 1432 96 126 279 -100 null
hh_Ab_Pinky2003_000010540 558 1228 1338 101 156 339 555 1012 1048 90 130 346 -100 null
hh_Ab_Pinky2003_000010558 850 1188 1142 104 139 203 494 761 847 89 104 108 -100 null
hh_Ab_Pinky2003_000010564 381 802 955 108 141 130 385 554 546 94 113 79 0 null
hh_Ab_Pinky2003_000010870 658 904 720 106 147 251 668 807 538 96 122 196 0 -0.05
hh_Ab_Pinky2003_000010876 388 1176 1732 109 139 116 371 930 1490 92 109 81 0 null
hh_Ab_Pinky2003_000010894 547 1036 1139 119 175 339 344 723 996 97 123 113 0 null
hh_Ab_Pinky2003_000010900 591 1245 1558 122 173 294 348 866 1341 97 121 108 0 0.99

Total number of rows: 16894

Table truncated, full table size 1381 Kbytes.




Supplementary file Size Download File type/resource
GSM569293_p4_10s014_JBC_20090315_genepix6.gpr.gz 1.8 Mb (ftp)(http) GPR
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap