|
| Status |
Public on Mar 22, 2007 |
| Title |
ChIP-chip examination of H3me2K4 in S. pombe wild-type |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
H3me2K4 immunoprecipitated DNA
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
Wild-type; h- strain
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
7 ul of the immunoprecipitated DNA or a 1/100 dilution of input DNA were subjected to two rounds of sequenase primer extension with primer A, and later PCR amplified for 40 cycles with primer B. The PCR product was purified using Qiaquick PCR purification columns, eluted in water and concentrated by vacuum centrifugation to 0.5 ug/ul.
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Sample labeling performed by NimbleGen Systems, Inc.
|
| |
|
| Channel 2 |
| Source name |
Wild-type control input DNA
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
Wild-type; h- strain
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
7 ul of the immunoprecipitated DNA or a 1/100 dilution of input DNA were subjected to two rounds of sequenase primer extension with primer A, and later PCR amplified for 40 cycles with primer B. The PCR product was purified using Qiaquick PCR purification columns, eluted in water and concentrated by vacuum centrifugation to 0.5 ug/ul.
|
| 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 H3me2K9 localization in a genomic context in the histone demethylase mutant lsd1. Genomic DNA was extracted after crosslinking from whole cell-extract and chromatin immunoprecipitated using an anti-H3me2K4 antibody
|
| Data processing |
Nimblegen-supplied data files were imported into the Bioconductor computing environment (http://bioconductor.org/). After performing quantile normalization, per-probe enrichments 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 ChIP-chip enrichment were computed by empirical Bayes shrinkage of the standard errors with the False Discovery Rate controlled to 0.05 using the method of Benjamini and Hochberg.
|
| |
|
| Submission date |
Jan 16, 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 |
|
