|
| Status |
Public on Nov 24, 2014 |
| Title |
ctk1Δ_Rpb3_SM_1 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
bur1as/ctk1Δ
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
treatment: Sulfometuron methyl
myc-tagged: STH1-MYC
antibody: Rpb3 (Neoclone: W0012)
sample type: ChIP DNA
|
| Treatment protocol |
The cells were either grown in SC or YPD. For inducing Gcn4, the cells were grown in SC and then treated with 0.65 µM of sulfometuron methyl (SM; Chemservice, cat# N-13254) for 20 minutes and processed for ChIP analysis. The kin28as/bur2Δ were treated with 1NA-PP1 and bur1as/ctk1Δ strains were treated with 3MB-PP1 before processing for cross-linking and chromatin preparation
|
| Growth protocol |
Chromatin immunoprecipitation experiments were performed as described previously (Govind et al., 2012). Briefly, 100 ml of cells (A600 = 0.6) were cross-linked with 1% formaldehyde for 15 minutes at ambient temperature and quenched with glycine. Chromatin was isolated and fragmented by sonication (Branson450) to an average size of 300-400 base pairs. The soluble fraction of chromatin was used for ChIP using the appropriate antibodies.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The ChIP and Input DNA was extracted by Phenol:Chloform method after reverse-crosslinking at 65 degree C, and after proteinase K treatment. DNA was fragmented with DNase prior to labeling
|
| Label |
Cy3
|
| Label protocol |
manufacturer's recommended protocol was followed
|
| |
|
| Channel 2 |
| Source name |
bur1as/ctk1Δ
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
parent strain: BY4142
strain: HQY1236
sample type: input
|
| Treatment protocol |
The cells were either grown in SC or YPD. For inducing Gcn4, the cells were grown in SC and then treated with 0.65 µM of sulfometuron methyl (SM; Chemservice, cat# N-13254) for 20 minutes and processed for ChIP analysis. The kin28as/bur2Δ were treated with 1NA-PP1 and bur1as/ctk1Δ strains were treated with 3MB-PP1 before processing for cross-linking and chromatin preparation
|
| Growth protocol |
Chromatin immunoprecipitation experiments were performed as described previously (Govind et al., 2012). Briefly, 100 ml of cells (A600 = 0.6) were cross-linked with 1% formaldehyde for 15 minutes at ambient temperature and quenched with glycine. Chromatin was isolated and fragmented by sonication (Branson450) to an average size of 300-400 base pairs. The soluble fraction of chromatin was used for ChIP using the appropriate antibodies.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The ChIP and Input DNA was extracted by Phenol:Chloform method after reverse-crosslinking at 65 degree C, and after proteinase K treatment. DNA was fragmented with DNase prior to labeling
|
| Label |
Cy5
|
| Label protocol |
manufacturer's recommended protocol was followed
|
| |
|
| |
| Hybridization protocol |
The samples were lableled using BioPrime Array CGH Genomic Labeling Module kit and hybridized according to the Manufacturer's recommended protocol
|
| Scan protocol |
Agilent Technologies Scanner G2505B US45102973
|
| Description |
Bological Replicate-1
|
| Data processing |
Data processed on R. Median normalization carried out.
|
| |
|
| Submission date |
Oct 20, 2014 |
| Last update date |
Nov 24, 2014 |
| Contact name |
Chhabi Govind |
| E-mail(s) |
[email protected]
|
| Organization name |
Oakland University
|
| Department |
Biological Sciences
|
| Street address |
333 Science and Engineering Building
|
| City |
Rochester |
| State/province |
mi |
| ZIP/Postal code |
48085 |
| Country |
USA |
| |
|
| Platform ID |
GPL10930 |
| Series (2) |
| GSE62519 |
The RSC Complex localizes to coding sequences to regulate Pol II and histone occupancy (Agilent) |
| GSE62522 |
The RSC Complex localizes to coding sequences to regulate Pol II and histone occupancy |
|
