GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM578362 Query DataSets for GSM578362
Status Public on Dec 09, 2011
Title Saccharomyces_cerevisiae-nucleosome-reads
Sample type SRA
Source name Saccharomyces cerevisiae
Organism Saccharomyces cerevisiae
Characteristics strain: BY4741
Treatment protocol Cells were then cross-linked with formaldehyde and mono-nucleosomes were isolated according to modified protocols from Lee, Tillo., et al. Nature Genetics (2007)
Growth protocol Cells were grown in YPD (2% peptone, 1% yeast extract, 2% dextrose) starting from a overnight culture until they reached mid-log phase (0.8 OD).
Extracted molecule genomic DNA
Extraction protocol Mono-nucleosomes were extracted by treating the cell spheroplast with Mnase. Samples representing mono-nucleosomes were gel extracted, end repaired and adapter ligated.
Library strategy MNase-Seq
Library source genomic
Library selection MNase
Instrument model Illumina Genome Analyzer II
Data processing The genome sequences were retrieved using SGD or Genolevures. Reads were mapped using Novocraft and only unique reads were further processed. As reads covered both ends of the ~150bp length DNA fragments that correspond to mono-nucleosomes, we converted the mapped positions into the estimated center position by adding or removing (depending on the strand) half the length of a typical DNA fragment. This typical length was evaluated in each sample by the distances between consecutive peaks of reads from the forward and backward strands, and was between 110bp to 130bp in all samples. For S. bayanus and C.glabrata, the reads from two biological repeats were combined into a single dataset. Data represents one-to-one orthologs which were defined based on Cliften et al. (Cliften, Sudarsanam et al. 2003) and Wapinski et al. (Wapinski, Pfeffer et al. 2007). Occupancy patterns were taken from -600 to +1000 (relative to the ATG) and for genes shorter than 1kb, we examined the pattern only until the end of the gene.
Submission date Aug 11, 2010
Last update date May 15, 2019
Contact name Kyle Tsui
Organization name University of Toronto
Lab HipHop
Street address 160 College Street
City Toronto
ZIP/Postal code M5S 3E1
Country Canada
Platform ID GPL9377
Series (1)
GSE23577 Nucleosome positioning for 4 yeast species
SRA SRX025556
BioSample SAMN00102769

Supplementary file Size Download File type/resource
GSM578362_Scerevisiae.txt.gz 4.2 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap