|
| Status |
Public on Feb 20, 2014 |
| Title |
Disome 5 ubp6∆ vs. wild-type |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Disome 5 ubp6∆
|
| Organism |
Saccharomyces cerevisiae W303 |
| Characteristics |
cell type: Disome 5 ubp6∆
age: day 1
|
| Growth protocol |
Cells grown in YEPD at 30 degrees
|
| Extracted molecule |
total RNA |
| Extraction protocol |
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 |
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 |
whole cells
|
| Organism |
Saccharomyces cerevisiae W303 |
| Characteristics |
cell type: whole cells
age: day 1
|
| Growth protocol |
Cells grown in YEPD at 30 degrees
|
| Extracted molecule |
total RNA |
| Extraction protocol |
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 |
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 |
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 |
Scanned on an Agilent G2505B
Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).
|
| Description |
Grown in YEPD at 30 degrees
|
| Data processing |
Agilent Feature Extractor A.7.5.1
|
| |
|
| Submission date |
Feb 19, 2014 |
| Last update date |
Feb 20, 2014 |
| Contact name |
Eduardo M Torres |
| E-mail(s) |
Eduardo.Torres@umassmed.edu
|
| Phone |
5088564353
|
| Organization name |
University of Massachusetts Medical School
|
| Department |
Department of Molecular, Cell and Cancer Biology
|
| Lab |
Torres
|
| Street address |
364 Plantation Street, LRB-523
|
| City |
worcester |
| State/province |
MA |
| ZIP/Postal code |
01605 |
| Country |
USA |
| |
|
| Platform ID |
GPL16244 |
| Series (1) |
| GSE55166 |
Disomes and Disomes ubp6∆ vs. wild-type |
|
