|
| Status |
Public on Jan 24, 2010 |
| Title |
Copper Exposed (60 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 |
Copper 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 : 60 minutes
Compound Based Treatment : 2 mM CuSO4
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 : 517
Pixel Size : 5
Laser on time : 20465
Laser Power : 10.00
Scan Date : 2007-12-01
Scan Temperature : 30.97
Scan Time : 18:12:03
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 |
Copper Exposed (60 min.)
|
| Data processing |
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 920, 3960
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 |
GPL8667 |
| 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. |
