|
| Status |
Public on Feb 28, 2013 |
| Title |
Nup170-myc ChIP from sir4∆ cells |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Nup170-myc ChIP from sir4∆ cells, ChIP
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
chip antibody: anti-Myc monoclonal antibody (cat# 9E10; Roche)
strain: YWY1501 (MATa his3∆1 leu2∆0 ura3∆0 lys2∆0 NUP170-9xMYC::hphR sir4∆::natR)
|
| Growth protocol |
Yeast strains were cultured at 30˚C in YPD medium to an OD600 of 1.0 and proteins were cross-linked to their respective DNA binding sites with 1% formaldehyde for 1 h at room temperature and the cross-linking reaction was quenched by incubation with 125 mM glycine for 5 min prior to harvesting of cells.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin immunoprecipitations were performed as described by Smith et al., 2007 with modifications according to Wan et al., 2009. Cells were disrupted by glass bead lysis and chromatin was sheared to an average size of 400 bp. Myc-tagged fusion proteins were purified using 2 μg of α-Myc antibody (9E10; Roche) prebound to 50 μl of Dynabead Pan Mouse IgG magnetic beads (Invitrogen) and incubated with sheared chromatin lysate containing 1 mg of protein overnight at 4˚C. Crosslinks were reversed in ChIP and whole cell lysate fractions and purified samples were analyzed by DNA microarrays.
|
| Label |
Cy5
|
| Label protocol |
Agilent yeast ChIP protocol
|
| |
|
| Channel 2 |
| Source name |
Whole cell extractof Nup170-9xMyc in sir4∆ cells
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
chip antibody: none (whole cell extract)
strain: YWY1501 (MATa his3∆1 leu2∆0 ura3∆0 lys2∆0 NUP170-9xMYC::hphR sir4∆::natR)
|
| Growth protocol |
Yeast strains were cultured at 30˚C in YPD medium to an OD600 of 1.0 and proteins were cross-linked to their respective DNA binding sites with 1% formaldehyde for 1 h at room temperature and the cross-linking reaction was quenched by incubation with 125 mM glycine for 5 min prior to harvesting of cells.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin immunoprecipitations were performed as described by Smith et al., 2007 with modifications according to Wan et al., 2009. Cells were disrupted by glass bead lysis and chromatin was sheared to an average size of 400 bp. Myc-tagged fusion proteins were purified using 2 μg of α-Myc antibody (9E10; Roche) prebound to 50 μl of Dynabead Pan Mouse IgG magnetic beads (Invitrogen) and incubated with sheared chromatin lysate containing 1 mg of protein overnight at 4˚C. Crosslinks were reversed in ChIP and whole cell lysate fractions and purified samples were analyzed by DNA microarrays.
|
| Label |
Cy3
|
| Label protocol |
Agilent yeast ChIP protocol
|
| |
|
| |
| Hybridization protocol |
Agilent yeast ChIP protocol
|
| Scan protocol |
Agilent yeast ChIP protocol
|
| Description |
Genome-wide localization of Nup170-9xMyc in sir4∆ cells
|
| Data processing |
Data extraction was performed using the Agilent Feature Extraction software. Bound probes were analyzed by the Agilent ChIP Analytics software according to the neighborhood model. In the neighborhood model, a probe to be considered as significantly bound was required to pass the following filters: 1) the candidate bound probe has a p-value ≤ 0.05, and 2) the central probe has a p-value ≤ 0.05 or at least one neighboring probe has a p-value ≤ 0.25. The purpose of neighborhood model is to identify which probes are most representative of binding events.
|
| |
|
| Submission date |
Mar 26, 2012 |
| Last update date |
Feb 28, 2013 |
| Contact name |
Yakun Wan |
| E-mail(s) |
ywansystemsbiology@gmail.com
|
| Organization name |
Southeast University
|
| Street address |
Sipailou #2
|
| City |
Nanjing |
| ZIP/Postal code |
210096 |
| Country |
China |
| |
|
| Platform ID |
GPL4131 |
| Series (2) |
| GSE36794 |
A role for the nucleoporin Nup170p in chromatin structure and gene silencing [Agilent ChIP-chip] |
| GSE36795 |
A role for the nucleoporin Nup170p in chromatin structure and gene silencing |
|
