|
| Status |
Public on Feb 28, 2013 |
| Title |
Genome-wide nucleosome positioning in sth1p_depletion_0h cells |
| Sample type |
SRA |
| |
|
| Source name |
Mnase-seq genomic DNA
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
genotype/variation: sth1p_depletion_0h
|
| Treatment protocol |
Cells were treated with 1% formaldehyde for 20 min, followed by a 5 min incubation with 125 mM glycine prior to cell harvesting.
|
| Growth protocol |
sth1p depletion cells were grown in YPD medium to an OD600 of 1.0
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cell permeablization, micrococcal nuclease digestion, protein degradation and DNA purification steps were performed as described in (Yuan et al., 2005). DNA samples were treated with RNase A and analyzed in a 2% agarose gel to quantify nucleosomal content. The bands corresponding to mononucleosomal DNA were extracted using a Qiagen gel extraction kit (Qiagen) and analyzed by Illumina sequencing (Illumina Inc.) as previously described (Shivaswamy et al., 2008 and Weiner et al., 2010).
|
| |
|
| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Typical digested Mnase-seq genomic DNA
|
| Data processing |
Reads were initially processed and mapped to the genomic sequences of S. cerevisiae by CASAVA software allowing up to two mismatches, and the raw profiles were further analyzed by our newly developed program to determine nucleosome profiles as follows. 1) all reads were first mapped to the genomic sequences of S. cerevisiae, 2) each read was extended toward the 3'-end to 150 nt, 3) the center of the extended reads (75th nucleotide) of all extended reads was then taken as each read's signal, and 4) in order to detect all fine-grained or coarse-grained peak calls, we design a flexible and customizable Gaussian filter that can define a series of Gaussian templates with different windows and standard deviations to infer possible nucleosome calls.
Genome_build: yeast S288C strain (NC_001138 - NC_001148)
|
| |
|
| Submission date |
Aug 13, 2012 |
| Last update date |
May 15, 2019 |
| 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 |
GPL9377 |
| Series (2) |
| GSE36792 |
The nucleoporin Nup170p is required for subtelomeric chromatin structure and gene silencing. [MNase-Seq] |
| GSE36795 |
A role for the nucleoporin Nup170p in chromatin structure and gene silencing |
|
| Relations |
| SRA |
SRX176304 |
| BioSample |
SAMN01113004 |
