|
| Status |
Public on Mar 22, 2007 |
| Title |
Transcriptional profilng of the S. pombe histone demethylase mutant lsd1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
lsd1- mutant
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
Wild-type; h- strain versus lsd1 deletion; h- strain
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from wild type and mutant cells cultured to mid-logaritmic phase was isolated using standard procedures. Copy DNA for labeling was produced from 10 ug of total RNA using the Superscript II Double Stranded cDNA synthesis kit (Invitrogen) with the provided OligodT primer, purified by Phenol:chloroform:isoamyl alchohol extraction and ethanol precipitation, then resuspended in water
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Sample labeling performed by NimbleGen Systems, Inc.
|
| |
|
| Channel 2 |
| Source name |
Wild-type total RNA
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
Wild-type; h- strain versus lsd1 deletion; h- strain
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from wild type and mutant cells cultured to mid-logaritmic phase was isolated using standard procedures. Copy DNA for labeling was produced from 10 ug of total RNA using the Superscript II Double Stranded cDNA synthesis kit (Invitrogen) with the provided OligodT primer, purified by Phenol:chloroform:isoamyl alchohol extraction and ethanol precipitation, then resuspended in water
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Sample labeling performed by NimbleGen Systems, Inc.
|
| |
|
| |
| Hybridization protocol |
Hybridization performed by NimbleGen Systems, Inc.
|
| Scan protocol |
Scanning performed by NimbleGen Systems, Inc.
|
| Description |
A reference design including a dye reversal was used to examine genome-wide expression levels in the histone demethylase mutant lsd1.
|
| Data processing |
Nimblegen-supplied data files were imported into the Bioconductor computing environment (http://bioconductor.org/). After performing quantile normalization, per-probe differences relative to wild-type were estimated for each probe by fitting a fixed linear model accounting for array, dye, and treatment effects to the data using the limma package (Smyth 2004). Moderated t-statistics and the log-odds score for differential expression was computed by empirical Bayes shrinkage of the standard errors with the False Discovery Rate controlled to 0.05 using the Benjamini-Hochberg method.
|
| |
|
| Submission date |
Jan 15, 2007 |
| Last update date |
Mar 22, 2007 |
| Contact name |
Matthew Wayne Vaughn |
| E-mail(s) |
vaughn@tacc.utexas.edu
|
| Phone |
(512) 232-7124
|
| Organization name |
University of Texas at Austin
|
| Department |
Texas Advanced Computing Center
|
| Lab |
Vaughn
|
| Street address |
10100 Burnet Rd
|
| City |
Austin |
| State/province |
TX |
| ZIP/Postal code |
78758 |
| Country |
USA |
| |
|
| Platform ID |
GPL4749 |
| Series (1) |
| GSE6753 |
Localization and mechanism of S. pombe histone demethylases |
|
