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Sample GSM415456 Query DataSets for GSM415456
Status Public on Jan 24, 2010
Title heat shock 15' (25-37)
Sample type RNA
 
Channel 1
Source name Pooled reference
Organism Saccharomyces bayanus
Characteristics species: S. bayanus
strain name: mixed
Biomaterial provider Sarah Pfau, 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 Experimental at 15'
Organism Saccharomyces bayanus
Characteristics strain name: ACY12
genotype: prototroph
sex/mating type: MATalpha
species: S. bayanus
Biomaterial provider Sarah Pfau, QCB301 project, Princeton University
Treatment protocol Time : 15 minutes
Growth Condition : 37C 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 Pixel Size : 5
Scan Date : 2006-09-21
Scan Time : 17:55:29
Scanner Make : Agilent Technologies Scanner
Scanner Model : G2505B
Scanning software : ChipScan
Scanning software version : A.6.3.1
Description heat shock 15' (25-37)
Data processing Extraction Software : GenePix Pro
Extraction Software Version : 6.0.1.25
Datafile type : GenePix Results 3
Image Origin : 0, 0
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 GPL8665
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 -1.474 .36 1838 662 1878 40 775 113 .98 0
2 .314 1.243 213 265 252 39 378 113 .88 0
3 .974 1.965 4130 8115 4169 39 8228 113 .99 0
4 .012 1.008 432 436 471 39 544 109 .94 0
5 .624 1.541 291 448 330 39 559 111 .95 0
6 -3.713 .076 28 2 68 40 113 111 -.03 0
7 -1.228 .427 15 6 55 40 120 113 .13 0
8 .277 1.212 731 886 771 40 999 113 .96 0
9 -.053 .964 558 538 600 42 653 115 .94 0
10 .393 1.313 1621 2129 1660 39 2242 113 .99 0
11 .094 1.067 192 205 230 38 316 111 .92 0
12 -.693 .618 656 406 692 36 517 111 .96 0
13 .451 1.367 998 1364 1034 36 1471 107 .98 0
14 -1.692 .309 69 21 107 38 128 107 .31 0
15 .31 1.24 2401 2976 2441 40 3087 111 .96 0
16 -.242 .845 5609 4742 5650 41 4857 115 .98 0
17 -.662 .632 939 594 978 39 705 111 .98 0
18 -.172 .888 1337 1187 1376 39 1300 113 .97 0
19 -.848 .556 73 41 113 40 152 111 .68 0
20 -1.525 .348 43 15 84 41 130 115 .32 0

Total number of rows: 11520

Table truncated, full table size 475 Kbytes.




Supplementary file Size Download File type/resource
GSM415456.gpr.gz 922.8 Kb (ftp)(http) GPR
Processed data included within Sample table

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