|
| Status |
Public on May 17, 2007 |
| Title |
Fig 1AB: Dis I (A6863) batch RNA 1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source Name |
11311A RNA
|
| Organism(s) |
Saccharomyces cerevisiae |
| Characteristics |
Strain Name : wt (A11311)
|
| Biomaterial provider |
Maitreya Dunham, Dunham Lab, Princeton University
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Description : Filters were incubated for 1 hour at 65oC in lysis buffer (10 mM EDTA, 0.5% SDS, and 10 mM Tris, pH 7.5) and acid phenol. The aqueous phase was further extracted twice with an equal volume of chloroform using phase lock gel (Eppendorf). Total RNA was then ethanol precipitated and further purified over RNeasy columns (Qiagen). RNA quality was checked using the Bioanalyzer RNA Nano kit.
|
| Label |
Cy3
|
| Label protocol |
Description : 325 ng was used for microarray labeling with the Agilent Low RNA Input Fluorescent Linear Amplification Kit. Reactions were performed as directed except using half the recommended reaction volume and one quarter the recommended Cy-CTP amount. Dye incorporation and yield were measured with a Nanodrop spectrophotometer.
|
| |
|
| Channel 2 |
| Source Name |
6863A RNA
|
| Organism(s) |
Saccharomyces cerevisiae |
| Characteristics |
Strain Name : Dis I (A6863)
|
| Biomaterial provider |
Maitreya Dunham, Dunham Lab, Princeton University
|
| Growth protocol |
Description : Cultures were grown overnight at 30C in selective -his/G418 media and then diluted back to OD=0.3 in 250 ml -his/G418 media. Cultures were grown shaking at 30C to midlog (OD=1.0-1.3) and harvested by vacuum filtration, flash-frozen in liquid nitrogen, and stored at ?80oC until RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Description : Filters were incubated for 1 hour at 65oC in lysis buffer (10 mM EDTA, 0.5% SDS, and 10 mM Tris, pH 7.5) and acid phenol. The aqueous phase was further extracted twice with an equal volume of chloroform using phase lock gel (Eppendorf). Total RNA was then ethanol precipitated and further purified over RNeasy columns (Qiagen). RNA quality was checked using the Bioanalyzer RNA Nano kit.
|
| Label |
Cy5
|
| Label protocol |
Description : 325 ng was used for microarray labeling with the Agilent Low RNA Input Fluorescent Linear Amplification Kit. Reactions were performed as directed except using half the recommended reaction volume and one quarter the recommended Cy-CTP amount. Dye incorporation and yield were measured with a Nanodrop spectrophotometer.
|
| |
|
| |
| Hybridization protocol |
Description : Equal masses of differentially labeled control and sample cRNA were combined such that each sample contained at least 2.5 pmol dye. Samples were mixed with control targets, fragmented, combined with hybridization buffer, and applied to a microarray consisting of 60mer probes for each yeast open reading frame (Agilent). Microarrays were rotated at 60?C for 17 hours in a hybridization oven (Agilent). Arrays were then washed according to the Agilent SSPE wash protocol, and scanned on an Agilent scanner.
|
| Scan protocol |
Pixel Size : 10
Scan Date : 2004-10-14
Scan Time : 11:15:42
Scanner Make : Agilent Technologies Scanner
Scanner Model : G2505B
Scanning software : ChipScan
Scanning software version : A.6.3.1
|
| Description |
former name: AA chr 1 disome (6863) RNA set 1
|
| Data processing |
Extraction Software : Agilent Feature Extractor
Extraction Software Version : A.7.5.1
Datafile type : Agilent result file
|
| |
|
| Submission date |
May 15, 2007 |
| Contact name |
Maitreya J. Dunham |
| E-mail(s) |
maitreya@u.washington.edu
|
| Phone |
206-543-2338
|
| URL |
http://dunham.gs.washington.edu
|
| 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 |
GPL884 |
| Series (1) |
| GSE7812 |
Torres et al 2007 (submitted) |
|
