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Sample GSM415465 Query DataSets for GSM415465
Status Public on Jan 24, 2010
Title Ethanol Exposure (0 min.)
Sample type RNA
 
Channel 1
Source name Mixed Reference
Organism Saccharomyces bayanus
Characteristics species: S. bayanus
strain name: mixed
Biomaterial provider Samuel Leachman, QCB301 project, Princeton University
Treatment protocol Growth Condition : mixed
Extracted molecule total RNA
Extraction protocol Extracted molecule : RNA
Extraction method : acid phenol extraction
Label Cy3
Label protocol reference URL : http://genomics.princeton.edu/caudylab/Yeast_RNA_Prep_and_Labeling_070925.pdf
 
Channel 2
Source name Ethanol Exposed
Organism Saccharomyces bayanus
Characteristics strain name: ACY12
genotype: prototroph
sex/mating type: MATalpha
species: S. bayanus
Biomaterial provider Samuel Leachman, QCB301 project, Princeton University
Treatment protocol Time : 0 minutes
Compound Based Treatment : 5% ethanol
Growth Condition : 25C YPD
Extracted molecule total RNA
Extraction protocol Extracted molecule : RNA
Extraction method : acid phenol extraction
Label Cy5
Label protocol reference URL : http://genomics.princeton.edu/caudylab/Yeast_RNA_Prep_and_Labeling_070925.pdf
 
 
Hybridization protocol reference URL : http://genomics.princeton.edu/caudylab/Yeast_RNA_Prep_and_Labeling_070925.pdf
Scan protocol Scan Power : 100
PMT Volts : 463
Pixel Size : 5
Laser on time : 18536
Laser Power : 8.63
Scan Date : 2007-11-21
Scan Temperature : 30.75
Scan Time : 15:33:55
Scanner Make : Axon Instruments (V1.00)
Scanner Model : GenePix 4000B [116465]
Scanning software : AxImageIO
Scanning software version : 2.0.3.2
Focus Position : 0
Description Ethanol Exposure (0 min.)
Data processing Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 1280, 3680
Normalization: Channel 2 values were scaled such that the average ratio for each array was set at 1. This scaling factor was calculated using only features from S. bayanus (some arrays also contain S. cerevisiae features that were not used for this project) with >65% of pixels >1 standard deviations above background in both channels.
 
Submission date Jun 10, 2009
Last update date Jul 11, 2013
Contact name Maitreya J. Dunham
E-mail(s) maitreya@uw.edu
Phone 206-543-2338
Organization name University of Washington
Department Genome Sciences
Lab Dunham Lab
Street address Foege Building, S403B, Box 355065
City Seattle
State/province WA
ZIP/Postal code 98195-5065
Country USA
 
Platform ID GPL8667
Series (2)
GSE16544 Systematic planning of genome-scale experiments in poorly studied species.
GSE47613 A New System for Comparative Functional Genomics of Saccharomyces Yeasts

Data table header descriptions
ID_REF
VALUE Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEAN)].
RAT2N_MEAN Channel 2/Channel 1 ratio normalized, RAT2_MEAN/Normalization factor or Red/Green mean ratio normalized.
CH1D_MEAN Mean Channel 1 (usually 532 nm) intensity with the median-background subtracted (CH1I_MEAN - CH1B_MEDIAN)
CH2DN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEAN - CH2BN_MEDIAN).
CH1I_MEAN Mean spot pixel intensity at Channel 1 (usually 532 nm).
CH1B_MEDIAN Median spot background intensity in Channel 1 (usually 532 nm).
CH2IN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).
CH2BN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).
CORR Sqrt(Coefficient of determination for the current regression value) with sign inferred from sign of REGR column. Value of '-1' indicates an error in this field.
FLAG Type of flag associated with a spot.

Data table
ID_REF VALUE RAT2N_MEAN CH1D_MEAN CH2DN_MEAN CH1I_MEAN CH1B_MEDIAN CH2IN_MEAN CH2BN_MEDIAN CORR FLAG
1 .807 1.749 623 1090 679 56 1161 71 .78 0
2 .691 1.614 380 613 433 53 685 71 .83 0
3 .633 1.551 605 938 658 53 1010 71 .79 0
4 .656 1.576 379 597 434 55 669 71 .65 0
5 .578 1.493 410 612 463 53 686 74 .75 0
6 .525 1.439 474 682 533 59 765 83 .7 0
7 .732 1.661 599 995 649 50 1065 70 .83 0
8 .77 1.706 451 769 502 51 839 70 .73 0
9 -.521 .697 23 16 68 45 80 64 .45 -50
10 .888 1.851 961 1779 1008 47 1845 66 .86 0
11 .466 1.381 77 106 122 45 168 61 .84 -50
12 -1.042 .486 9 4 53 44 66 61 .27 -50
13 .634 1.552 2697 4186 2744 47 4250 64 .9 0
14 .532 1.446 679 982 727 48 1049 67 .84 0
15 .456 1.371 68 93 112 44 154 61 .76 -50
16 .847 1.799 849 1527 895 46 1591 64 .83 0
17 1.486 2.801 271 759 320 49 828 68 .8 0
18 -1.192 .438 263 115 310 47 181 66 .73 -50
19 -.028 .981 832 816 882 50 883 67 .83 0
20 .729 1.658 334 554 383 49 621 67 .82 0

Total number of rows: 12288

Table truncated, full table size 491 Kbytes.




Supplementary file Size Download File type/resource
GSM415465.gpr.gz 959.0 Kb (ftp)(http) GPR
Processed data included within Sample table

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