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Sample GSM480813 Query DataSets for GSM480813
Status Public on Dec 09, 2009
Title p4_06s40_20071112GJd
Sample type genomic
 
Channel 1
Source name Protomelas similis
Organism Protomelas similis
Characteristics test: Protomelas similis
Biomaterial provider Joyce collections
Treatment protocol none
Growth protocol field collections
Extracted molecule genomic DNA
Extraction protocol ProteinaseK/Phenol Extraction
Label Cy3
Label protocol dCTP incorporation with Klenow
 
Channel 2
Source name Astatotilapia burtoni
Organism Haplochromis burtoni
Characteristics reference: Astatotilapia burtoni
Biomaterial provider Renn lab stock
Treatment protocol none
Growth protocol standard captivity
Extracted molecule genomic DNA
Extraction protocol ProteinaseK/Phenol Extraction
Label Cy5
Label protocol dCTP incorporation with Klenow
 
 
Hybridization protocol The samples were combined with hybridization buffer (3.4X SSC, 0.15% SDS, 1 mM DTT, Cot-1DNA) and hybridized to the microarray at 67.5°C
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=780_690 ScanPower=100_100
Description Cy3= Protomelas similis genomic DNA Cy5= Astatotilapia burtoni genomic DNA hybed by G Jui in 2007
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 in R/Bioconductor with within-arrays loess (using a set of 250 conserved genes) and intensity ratios were calculated.
 
Submission date Dec 07, 2009
Last update date Dec 08, 2009
Contact name Suzy C.P. Renn
E-mail(s) [email protected]
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)
GSE19368 Malawi Duplication 20091207

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 normalized ratio Cy5/Cy3

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 1299 1355 364 370 378 112 2151 2152 714 771 783 134 0 null
hh_Ab_Pinky2003_000010108 629 967 743 352 359 101 1051 1529 1034 735 742 107 0 null
hh_Ab_Pinky2003_000010126 555 741 508 352 359 98 1043 1289 733 738 745 96 0 null
hh_Ab_Pinky2003_000010132 1263 1268 584 366 384 126 2019 2195 928 773 775 134 0 null
hh_Ab_Pinky2003_000010150 1577 1553 443 376 610 1590 1933 1843 631 759 873 375 -100 null
hh_Ab_Pinky2003_000010156 1319 1398 660 383 393 110 2156 2150 973 778 788 118 -100 null
hh_Ab_Pinky2003_000010174 1100 1044 462 371 399 168 1198 1185 308 773 790 143 0 null
hh_Ab_Pinky2003_000010180 792 837 261 362 375 132 1574 1621 537 754 763 118 0 null
hh_Ab_Pinky2003_000010486 1020 1124 507 359 370 106 1880 2037 667 762 764 105 -100 null
hh_Ab_Pinky2003_000010492 1263 1242 601 415 429 143 1946 2070 892 778 816 202 0 null
hh_Ab_Pinky2003_000010510 1547 1609 717 406 421 149 3179 2838 1078 787 820 234 -100 null
hh_Ab_Pinky2003_000010516 2489 7037 8955 373 385 109 2887 8495 10637 765 772 132 0 0.361286595405408
hh_Ab_Pinky2003_000010534 1337 1457 554 376 392 222 1951 2178 774 763 779 522 0 0.089441728068703
hh_Ab_Pinky2003_000010540 678 715 216 356 400 405 1449 1403 376 756 824 1021 0 null
hh_Ab_Pinky2003_000010558 1939 2170 1045 371 385 207 2291 2476 880 756 764 168 0 0.451781453394432
hh_Ab_Pinky2003_000010564 995 1049 347 370 377 93 1721 1691 545 761 763 97 0 -0.278725665042381
hh_Ab_Pinky2003_000010870 1067 1170 455 371 380 100 1688 1836 563 755 759 98 0 -0.0793666488387875
hh_Ab_Pinky2003_000010876 777 1251 1190 374 385 98 1160 1470 796 759 761 95 0 null
hh_Ab_Pinky2003_000010894 1715 4131 5180 369 376 96 1694 3217 3256 759 767 95 0 null
hh_Ab_Pinky2003_000010900 1936 1999 658 375 379 97 2929 3025 938 764 761 88 0 -0.0670318444667495

Total number of rows: 16894

Table truncated, full table size 1491 Kbytes.




Supplementary file Size Download File type/resource
GSM480813.gpr.gz 1.8 Mb (ftp)(http) GPR
Processed data included within Sample table
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