|
| Status |
Public on Sep 15, 2010 |
| Title |
∆nhp6A ∆nhp6B vs Nhp6A ∆nhp6B, replicate 2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Saccharomyces cerevisiae
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
genotype/variation: NHP6A ∆nhp6B
|
| Growth protocol |
Asynchronously dividing cells (OD ~ 1.0) growing at 30ºC in rich media (YP with 2% glucose).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from cells using the hot phenol method (Köhrer and Domdey 1991). Total RNA was further isolated from genomic DNA using the Qiagen Rneasy Plus Mini Kit (# 74134).
|
| Label |
Cy3
|
| Label protocol |
The Agilent Quick Amp Two-color Labeling Kit (# 5190-0444) was used to fluorescently label the RNA.
|
| |
|
| Channel 2 |
| Source name |
Saccharomyces cerevisiae
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
genotype/variation: ∆nhp6A ∆nhp6B
|
| Growth protocol |
Asynchronously dividing cells (OD ~ 1.0) growing at 30ºC in rich media (YP with 2% glucose).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from cells using the hot phenol method (Köhrer and Domdey 1991). Total RNA was further isolated from genomic DNA using the Qiagen Rneasy Plus Mini Kit (# 74134).
|
| Label |
Cy5
|
| Label protocol |
The Agilent Quick Amp Two-color Labeling Kit (# 5190-0444) was used to fluorescently label the RNA.
|
| |
|
| |
| Hybridization protocol |
The Agilent protocol (chem.agilent.com) was followed for labeling and hybridizing the cDNA to the 4 x 44K (V1) S. cerevisiae gene expression arrays.
|
| Scan protocol |
The arrays were scanned on the Agilent G2565BA fluorescent scanner.
|
| Description |
Asynchronously dividing cells (OD ~ 1.0) growing at 30ºC
|
| Data processing |
Data extraction and quality assessment was performed with Agilent Feature Extraction Software (version 10.5.1.1). Log ratio values are present in the Agilent Feature Extraction files provided. Identification of genes differentially expressed between wild-type and mutant strains was done in R using the limma package (Smyth et al. 2005). All data (minimum of two biological replicates) was loess normalized and background subtracted within each array and fit to a linear model with a simple design matrix comparing mutant signals to wild-type signals (Smyth and Speed 2003; Smyth 2004; Ritchie et al. 2007). An empirical Bayes method was used to calculate a moderated t-statistic and the associated P-values (Smyth 2004). The Benjamini and Hochberg method was used to control the false discovery rate, and differentially expressed genes were analyzed using the S. cerevisiae Genome Database for Gene Ontology enrichment (Hochberg and Benjamini 1990; Dwight et al. 2002).
|
| |
|
| Submission date |
Aug 13, 2010 |
| Last update date |
Aug 13, 2010 |
| Contact name |
Noah L. Dowell |
| E-mail(s) |
noahd@ucla.edu
|
| Organization name |
UCLA
|
| Department |
Biological Chemistry
|
| Street address |
615 Charles E. Young Drive South, BSRB 357
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL7542 |
| Series (2) |
| GSE23607 |
Transcriptional regulation through DNA bending by Nhp6A [Agilent] |
| GSE23608 |
Chromatin-dependent binding of the S. cerevisiae HMGB protein Nhp6A affects nucleosome dynamics and transcription |
|
