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Sample GSM569298 Query DataSets for GSM569298
Status Public on Jul 24, 2010
Title p4_10s050_MES_20090328_genepix6.gpr
Sample type RNA
 
Channel 1
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 Cy3
Label protocol Message Amp II with single round amplification
 
Channel 2
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 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=720_520 ScanPower=100_100
Description Cy3= Julidochromis transcriptus male aRNA Cy5= Julidochromis transcriptus 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 142 159 89 149 324 705 165 198 139 167 346 764 -50 null
hh_Ab_Pinky2003_000010108 1638 4318 5177 140 187 151 1927 4389 4644 170 236 241 -100 null
hh_Ab_Pinky2003_000010126 1172 4644 6967 115 147 216 907 3682 5031 120 156 143 0 null
hh_Ab_Pinky2003_000010132 718 5669 8635 99 108 65 397 4046 5942 103 117 49 -100 null
hh_Ab_Pinky2003_000010150 3239 6156 7624 89 104 66 1316 4352 5191 96 108 50 -100 null
hh_Ab_Pinky2003_000010156 1656 3237 3871 95 112 70 1644 2738 3313 98 113 55 -100 null
hh_Ab_Pinky2003_000010174 834 4419 6769 82 100 66 699 3612 5114 88 103 59 -100 null
hh_Ab_Pinky2003_000010180 1886 3974 5127 106 130 91 1556 2858 3688 107 129 72 -100 null
hh_Ab_Pinky2003_000010486 5935 10197 10657 105 119 72 3427 6956 7805 97 111 53 -100 null
hh_Ab_Pinky2003_000010492 352 3237 6609 100 112 61 283 2409 5117 100 116 55 0 0.36
hh_Ab_Pinky2003_000010510 2896 6658 9052 87 102 71 672 3625 4519 92 112 63 -100 null
hh_Ab_Pinky2003_000010516 147 484 1181 110 466 1953 146 448 1009 105 422 1845 0 null
hh_Ab_Pinky2003_000010534 1966 2798 4182 96 125 154 1100 2341 2745 94 106 74 -100 null
hh_Ab_Pinky2003_000010540 6881 9741 10777 84 105 75 4346 6763 7228 87 100 50 -100 null
hh_Ab_Pinky2003_000010558 692 3993 7105 97 112 68 602 3054 4934 100 113 48 0 0.13
hh_Ab_Pinky2003_000010564 7182 10738 10548 98 113 71 3985 6079 6035 101 111 44 -100 null
hh_Ab_Pinky2003_000010870 1910 2565 2010 104 119 73 1811 2356 1648 104 116 55 0 0.22
hh_Ab_Pinky2003_000010876 1804 7771 10435 102 127 118 1323 5811 8035 108 131 91 -100 null
hh_Ab_Pinky2003_000010894 1754 6274 9771 91 107 60 1619 3770 4638 103 116 49 -100 null
hh_Ab_Pinky2003_000010900 468 2286 4395 108 119 64 519 1930 3204 103 114 46 0 -0.33

Total number of rows: 16894

Table truncated, full table size 1422 Kbytes.




Supplementary file Size Download File type/resource
GSM569298_p4_10s050_MES_20090328_genepix6.gpr.gz 1.9 Mb (ftp)(http) GPR
Processed data included within Sample table

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