|
| Status |
Public on Jul 01, 2016 |
| Title |
cmr1Δ_Rpb3_2 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
IP
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: cmr1delta
tag: untagged
antibodies: Rpb3 (Neoclone: W0012)
|
| Treatment protocol |
The cells were grown in SC and induced for Gcn4, by treating cells grown in SC with with 0.65 µM of sulfometuron methyl (SM; Chemservice, cat# N-13254) for 20 minutes and processed for ChIP analysis.
|
| 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 |
Alexa555
|
| Label protocol |
BioPrime Array CGH Genomic Labeling Module was used for labeling and the manufacturer's recommended protocol was followed.
|
| |
|
| Channel 2 |
| Source name |
input
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: cmr1delta
tag: untagged
|
| Treatment protocol |
The cells were grown in SC and induced for Gcn4, by treating cells grown in SC with with 0.65 µM of sulfometuron methyl (SM; Chemservice, cat# N-13254) for 20 minutes and processed for ChIP analysis.
|
| 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 |
Alexa647
|
| Label protocol |
BioPrime Array CGH Genomic Labeling Module was used for labeling and the 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 |
Sulfometuron methyl
Biological Replicate-2
|
| Data processing |
Data processed on R. Median normalization carried out.
|
| |
|
| Submission date |
Jan 20, 2016 |
| Last update date |
Jul 01, 2016 |
| 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 (1) |
| GSE77016 |
Recruitment of Saccharomyces cerevisiae Cmr1/Ydl156w to coding regions promotes transcription genome wide |
|
