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Sample GSM415544 Query DataSets for GSM415544
Status Public on Jan 24, 2010
Title zeocin 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 zeocin 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 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 : 11:46:41
Scanner Make : Agilent Technologies Scanner
Scanner Model : G2505B
Scanning software : ChipScan
Scanning software version : A.7.0.1
Description zeocin 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 -.319 .802 688 552 740 52 585 34 .69 0
2 -.201 .87 513 446 563 50 479 33 .91 0
3 -.215 .862 758 653 811 53 686 33 .88 0
4 -.28 .824 776 639 827 51 672 33 .88 0
5 -.219 .859 777 667 830 53 701 34 .89 0
6 -.24 .847 898 760 952 54 795 34 .88 0
7 -.221 .858 772 663 824 52 695 33 .88 0
8 -.254 .838 969 813 1023 54 845 33 .89 0
9 -.256 .837 1371 1148 1409 38 1182 34 .95 0
10 -.012 .992 1967 1951 2021 54 1988 37 .94 0
11 -.225 .855 547 468 580 33 499 32 .94 0
12 -1.669 .315 311 98 355 44 133 35 .88 0
13 -.047 .968 1997 1933 2049 52 1970 37 .93 0
14 -.174 .886 2126 1884 2177 51 1918 34 .95 0
15 1.554 2.936 325 954 374 49 986 32 .9 0
16 .077 1.055 1396 1473 1431 35 1507 34 .96 0
17 -.092 .938 424 398 473 49 424 26 .93 0
18 .685 1.607 306 492 341 35 518 27 .91 0
19 .635 1.553 35 54 66 31 78 23 .76 0
20 .294 1.226 2034 2493 2082 48 2520 27 .95 0

Total number of rows: 12672

Table truncated, full table size 511 Kbytes.




Supplementary file Size Download File type/resource
GSM415544.gpr.gz 1.1 Mb (ftp)(http) GPR
Processed data included within Sample table

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