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Sample GSM415543 Query DataSets for GSM415543
Status Public on Jan 24, 2010
Title zeocin 15 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 zeocin 15 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 : 15 minutes
Compound Based Treatment : 1 ug/mL zeocin
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 : 2008-02-29
Scan Time : 11:37:33
Scanner Make : Agilent Technologies Scanner
Scanner Model : G2505B
Scanning software : ChipScan
Scanning software version : A.7.0.1
Description zeocin 15 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 -.276 .826 793 655 822 29 676 21 .94 0
2 -.321 .801 641 513 672 31 535 22 .92 0
3 -.217 .86 924 795 956 32 817 22 .89 0
4 -.257 .837 533 446 565 32 467 21 .93 0
5 -.183 .881 858 756 890 32 776 21 .88 0
6 -.246 .843 845 713 878 33 733 20 .9 0
7 -.294 .816 1389 1133 1421 32 1153 20 .93 0
8 -.232 .852 902 768 934 32 788 20 .91 0
9 .01 1.007 2004 2018 2036 32 2038 21 .92 0
10 .093 1.066 1381 1473 1412 31 1494 21 .94 0
11 -.446 .734 683 502 712 29 520 18 .93 0
12 -2.15 .225 491 111 520 29 130 20 .91 0
13 -.104 .931 2451 2281 2477 26 2301 20 .94 0
14 -.292 .817 3139 2564 3164 25 2583 19 .95 0
15 1.4 2.639 420 1109 444 24 1127 18 .93 0
16 -.051 .965 1590 1535 1616 26 1555 20 .96 0
17 -.124 .918 471 432 504 33 452 19 .91 0
18 .93 1.905 294 560 326 32 579 19 .91 0
19 .342 1.267 53 67 83 30 85 18 .75 0
20 .284 1.218 1807 2201 1837 30 2219 18 .94 0

Total number of rows: 12672

Table truncated, full table size 527 Kbytes.




Supplementary file Size Download File type/resource
GSM415543.gpr.gz 1.1 Mb (ftp)(http) GPR
Processed data included within Sample table

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