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Sample GSM415671 Query DataSets for GSM415671
Status Public on Jan 24, 2010
Title 26.5hrs time point sporulation of S.b. BB10
Sample type RNA
 
Channel 1
Source name time point mixture
Organism Saccharomyces bayanus
Characteristics species: S. bayanus
strain name: BB10
Biomaterial provider Jenny Jia, Caudy Lab, Lewis-Sigler Institute for Integrative Genomics
Treatment protocol Growth Condition : mixed timepoints
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 26.5hrs in sporulation media
Organism Saccharomyces bayanus
Characteristics strain name: BB10
genotype: prototroph
sex/mating type: MATa/alpha
species: S. bayanus
Biomaterial provider Jenny Jia, Caudy Lab, Lewis-Sigler Institute for Integrative Genomics
Treatment protocol Time : 26.5 hours
Growth Condition : 25C SPO++
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 : 511
Pixel Size : 5
Laser on time : 27821
Laser Power : 10.00
Scan Date : 2007-12-21
Scan Temperature : 29.93
Scan Time : 11:38:37
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 26.5hrs time point sporulation of S.b. BB10
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 GPL8669
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 .644 1.563 2 3 45 43 51 48 -.08 0
2 2 0 44 42 49 49 -1 -50
3 -.941 .521 2 1 45 43 50 49 -1 -50
4 2 0 45 43 50 50 -1 -50
5 -.526 .694 3 2 46 43 51 49 -1 -50
6 2 -1 45 43 48 49 -1 0
7 -.941 .521 2 1 45 43 50 49 -1 -50
8 3 -2 47 44 48 50 -.03 0
9 2 0 45 43 49 49 -1 -50
10 0 -1 45 45 49 50 -1 0
11 .059 1.042 2 2 45 43 52 50 -1 -50
12 3 0 45 42 50 50 -.04 0
13 0 1 43 43 49 48 -.03 -50
14 3 0 45 42 48 48 -.03 -50
15 -1.941 .26 4 1 46 42 49 48 -.04 -50
16 .059 1.042 2 2 45 43 50 48 .12 -50
17 .059 1.042 1 1 44 43 50 49 -.03 -50
18 -1.526 .347 3 1 46 43 50 49 .04 0
19 3 0 46 43 50 50 .03 -50
20 -.465 .725 23 17 66 43 67 50 .69 0

Total number of rows: 12288

Table truncated, full table size 507 Kbytes.




Supplementary file Size Download File type/resource
GSM415671.gpr.gz 1004.6 Kb (ftp)(http) GPR
Processed data included within Sample table
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