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Sample GSM415463 Query DataSets for GSM415463
Status Public on Jan 24, 2010
Title sorbitol 20 mins
Sample type RNA
 
Channel 1
Source name reference
Organism Saccharomyces bayanus
Characteristics species: S. bayanus
strain name: mixed
Biomaterial provider Jenny Jia, Caudy Lab, Lewis-Sigler Institute for Integrative Genomics
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 sorbitol 20 mins
Organism Saccharomyces bayanus
Characteristics strain name: ACY12
genotype: prototroph
sex/mating type: MATalpha
species: S. bayanus
Biomaterial provider Jenny Jia, Caudy Lab, Lewis-Sigler Institute for Integrative Genomics
Treatment protocol Time : 20 minutes
Compound Based Treatment : 1 M sorbitol
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 Pixel Size : 5
Scan Date : 2008-03-06
Scan Time : 11:13:25
Scanner Make : Agilent Technologies Scanner
Scanner Model : G2505B
Scanning software : ChipScan
Scanning software version : A.7.0.1
Description sorbitol 20 mins
Data processing Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
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 GPL8493
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 -.259 .836 1713 1431 1761 48 1500 69 .91 0
2 -.43 .742 1622 1204 1669 47 1271 67 .92 0
3 -.353 .783 1013 793 1059 46 861 68 .91 0
4 -.438 .738 2173 1604 2221 48 1674 69 .9 0
5 -.397 .759 2151 1633 2198 47 1704 71 .9 0
6 -.465 .724 2636 1909 2684 48 1981 72 .91 0
7 -.289 .819 2411 1974 2459 48 2044 70 .9 0
8 -.386 .765 2313 1770 2360 47 1837 67 .91 0
9 .955 1.938 2361 4576 2408 47 4649 73 .89 0
10 -1.29 .409 3095 1265 3145 50 1335 69 .91 0
11 -.502 .706 590 417 637 47 484 68 .9 0
12 -1.223 .428 411 176 460 49 245 69 .82 0
13 .136 1.099 2495 2741 2545 50 2813 72 .87 0
14 -.022 .985 2254 2220 2302 48 2288 69 .91 0
15 -.932 .524 1072 562 1119 47 629 67 .92 0
16 .445 1.361 1341 1826 1389 48 1894 69 .92 0
17 .216 1.161 686 797 731 45 842 45 .89 0
18 -.333 .794 867 688 914 47 734 45 .89 0
19 .203 1.151 117 135 162 45 180 45 .75 0
20 .243 1.183 3323 3932 3369 46 3981 49 .88 0

Total number of rows: 12672

Table truncated, full table size 534 Kbytes.




Supplementary file Size Download File type/resource
GSM415463.gpr.gz 1.1 Mb (ftp)(http) GPR
Processed data included within Sample table

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