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Sample GSM984792 Query DataSets for GSM984792
Status Public on Feb 28, 2013
Title Genome-wide nucleosome positioning in sth1p_depletion_2h cells
Sample type SRA
Source name Mnase-seq genomic DNA
Organism Saccharomyces cerevisiae
Characteristics genotype/variation: sth1p_depletion_2h
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
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
SRA SRX176305
BioSample SAMN01113005

Supplementary file Size Download File type/resource
GSM984792_sth1p_depletion_2h.aligned.txt.gz 118.8 Mb (ftp)(http) TXT
GSM984792_sth1p_depletion_2h.gff.gz 995.0 Kb (ftp)(http) GFF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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