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Sample GSM901171 Query DataSets for GSM901171
Status Public on Feb 28, 2013
Title Nup157-myc ChIP from wild type cells
Sample type genomic
 
Channel 1
Source name Nup157-myc ChIP from wild type cells, ChIP
Organism Saccharomyces cerevisiae
Characteristics chip antibody: anti-Myc monoclonal antibody (cat# 9E10; Roche)
strain: YWY953 (MATa his3∆1 leu2∆0 ura3∆0 lys2∆0 NUP157-9xMYC::hphR)
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 Nup157-9xMyc
Organism Saccharomyces cerevisiae
Characteristics chip antibody: none (whole cell extract)
strain: YWY953 (MATa his3∆1 leu2∆0 ura3∆0 lys2∆0 NUP157-9xMYC::hphR)
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 Nup157-9xMyc
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

Data table header descriptions
ID_REF
VALUE Normalized log2 ratio (test/reference)
P-value

Data table
ID_REF VALUE P-value
12 -0.072693266 0.14669444
13 0.31422624 0.30171296
14 0.46951416 0.0987054
15 -0.024924662 0.23906443
16 -0.3725004 0.727006
17 -0.188994 0.38151518
18 0.27932775 0.089486174
19 -0.017692197 0.49884835
20 -0.22283316 0.82811254
21 0.1921417 0.62580854
22 -1.1256176 0.97523326
23 -0.09205616 0.59089863
24 0.3027643 0.27208185
25 -0.17198044 0.31309202
26 0.03812984 0.045544825
27 0.2920699 0.33543956
28 -0.35688123 0.74807394
29 -0.1652046 0.4231078
30 -0.60813 0.77846396
31 -0.3268119 0.28847232

Total number of rows: 41775

Table truncated, full table size 1123 Kbytes.




Supplementary file Size Download File type/resource
GSM901171_wt_nup157.tsv.gz 6.1 Mb (ftp)(http) TSV
Processed data included within Sample table
Processed data provided as supplementary file

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