NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM415496 Query DataSets for GSM415496
Status Public on Jan 24, 2010
Title Lead Exposure (20 min.)
Sample type RNA
 
Channel 1
Source name Mixed Reference
Organism Saccharomyces bayanus
Characteristics species: S. bayanus
strain name: mixed
Biomaterial provider Samuel Leachman, 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 Exposed
Organism Saccharomyces bayanus
Characteristics strain name: ACY12
genotype: prototroph
sex/mating type: MATalpha
species: S. bayanus
Biomaterial provider Samuel Leachman, QCB301 project, Princeton University
Treatment protocol Time : 20 minutes
Compound Based Treatment : 2 mM PbCl2
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 Scan Power : 100
PMT Volts : 484
Pixel Size : 5
Laser on time : 23758
Laser Power : 10.00
Scan Date : 2007-12-13
Scan Temperature : 31.21
Scan Time : 15:37:54
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 Lead Exposure (20 min.)
Data processing Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 1520, 4880
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 .46 1.376 467 642 521 54 721 78 .95 0
2 .559 1.474 1 1 52 51 74 72 .71 -50
3 1 0 51 50 72 72 -1 -50
4 .441 1.357 114 155 165 51 227 72 .94 -50
5 .559 1.474 1 1 52 51 74 72 .03 -50
6 1 -1 52 51 71 72 -.03 -50
7 1 0 51 50 71 71 -1 -50
8 .52 1.434 446 640 497 51 712 72 .95 0
9 .559 1.474 1 1 51 50 72 71 -1 -50
10 3 0 53 50 72 72 -.03 -50
11 .952 1.934 36372 70352 36424 52 70428 75 .98 0
12 5.051 33.156 2 66 53 51 137 71 .03 -50
13 .946 1.927 13 25 62 49 96 71 .21 -50
14 -.822 .566 99 56 148 49 127 71 .78 -50
15 1.559 2.947 5 15 55 50 85 71 .03 -50
16 1.729 3.316 4 13 54 50 84 71 .33 -50
17 .559 1.474 2 3 53 51 75 72 .03 -50
18 4.019 16.21 3 49 54 51 121 72 .07 -50
19 1.559 2.947 1 3 52 51 75 72 -.03 -50
20 5.26 38.313 1 38 52 51 111 72 .43 -50

Total number of rows: 12288

Table truncated, full table size 517 Kbytes.




Supplementary file Size Download File type/resource
GSM415496.gpr.gz 971.1 Kb (ftp)(http) GPR
Processed data included within Sample table
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap