NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1330663 Query DataSets for GSM1330663
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

Data table header descriptions
ID_REF
VALUE lowess normalized log2 ratio (Cy5/Cy3) representing disome/wt

Data table
ID_REF VALUE
A_06_P6355 0.4
A_06_P4350 -0.04
A_06_P7031 -0.43
A_06_P3477 -0.56
A_06_P2511 -0.52
A_06_P2222 1.22
A_06_P3673 0.49
A_06_P2925 -0.1
A_06_P6958 -0.07
A_06_P1955 0.3
A_06_P1986 -0.49
A_06_P5212 -0.32
A_06_P3975 0.45
A_06_P1699 1.04
A_06_P1085 -0.21
A_06_P6968 -0.55
A_06_P6837 0.03
A_06_P6055 0.12
A_06_P1095 0.36
A_06_P4807 -0.3

Total number of rows: 6237

Table truncated, full table size 97 Kbytes.




Supplementary file Size Download File type/resource
GSM1330663_dis5ubp6.txt.gz 1.3 Mb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap