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Sample GSM415466 Query DataSets for GSM415466
Status Public on Jan 24, 2010
Title Ethanol Exposure (5 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 : 5 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 : 468
Pixel Size : 5
Laser on time : 18563
Laser Power : 8.66
Scan Date : 2007-11-21
Scan Temperature : 30.75
Scan Time : 16:00:59
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 (5 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 .826 1.773 450 798 496 46 873 75 .7 0
2 .887 1.849 376 695 424 48 774 79 .73 0
3 .67 1.591 564 897 614 50 977 80 .77 0
4 .83 1.778 456 811 507 51 892 82 .73 0
5 .63 1.548 352 545 399 47 622 77 .67 0
6 .907 1.875 323 606 378 55 697 91 .64 0
7 .928 1.903 378 719 424 46 796 77 .69 0
8 .781 1.719 413 710 462 49 790 80 .64 0
9 -.237 .848 17 14 59 42 82 67 .45 -50
10 .599 1.515 679 1029 723 44 1101 72 .78 0
11 .274 1.209 53 64 95 42 131 67 .74 -50
12 -.32 .801 4 3 46 42 70 67 .27 -50
13 1.02 2.028 1952 3959 1997 45 4033 74 .79 0
14 .541 1.455 456 663 501 45 734 70 .7 0
15 .365 1.288 56 72 98 42 139 67 .72 -50
16 .376 1.298 784 1017 829 45 1090 72 .77 0
17 1.031 2.044 127 260 170 43 330 70 .83 -50
18 -.89 .54 196 106 239 43 175 69 .8 -50
19 .657 1.577 628 990 672 44 1062 72 .79 0
20 .505 1.419 131 186 174 43 255 69 .82 -50

Total number of rows: 12288

Table truncated, full table size 490 Kbytes.




Supplementary file Size Download File type/resource
GSM415466.gpr.gz 944.5 Kb (ftp)(http) GPR
Processed data included within Sample table
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