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Sample GSM694155 Query DataSets for GSM694155
Status Public on Apr 24, 2012
Title Log Unfixed Narrow Mnase-seq
Sample type SRA
 
Source name Log phase Pombe
Organism Schizosaccharomyces pombe
Characteristics strain: D18
plasmid: pLS-LCS1+2+3
growth phase: Log Phase
fixation: Unfixed
band excised: narrow
Treatment protocol Fixed samples were prepared by adding 0.0423 volumes of 37% w/w formaldehyde (Fisher Scientific # F79-500) to each volume of culture, to achieve a final (taking the added volume into account) concentration of 1.5% formaldehyde, then allowing incubation to continue with rotary agitation for 15 minutes.
Growth protocol The cells were grown in minimal medium at 25°C with 200-rpm agitation to either log phase (5-8×106 cells/ml ) or stationary phase (1-2×108 cells/ml), as required.
Extracted molecule genomic DNA
Extraction protocol Cryoground isolated nuclei were digested with MNase at 25C at various concentrations. The DNA was isolated and size selected by agarose gel. The band representing mono-nucleosomal DNA was isolated, purified, and processed for sequencing using the standard Illumina protocol.
 
Library strategy MNase-Seq
Library source genomic
Library selection MNase
Instrument model Illumina Genome Analyzer II
 
Description Mnase-seq for unfixed Log phase Pombe with narrow band excised
Data processing Sequencing reads were aligned to the August, 2008, build of the S. pombe genome (http://www.sanger.ac.uk/Projects/S_pombe/) using the BowTie algorithm ( http://bowtie-bio.sourceforge.net/index.shtml), allowing only unique matches with up to two possible mismatches.
 
Submission date Mar 21, 2011
Last update date Jun 11, 2013
Contact name Michael Buck
E-mail(s) mjbuck@buffalo.edu
Phone 7168817569
Organization name SUNY at Buffalo
Department Biochemistry
Street address 701 Ellicott St
City Buffalo
State/province NY
ZIP/Postal code 14203
Country USA
 
Platform ID GPL9453
Series (1)
GSE28071 Chromatin architectures at fission yeast transcriptional promoters and replication origins
Relations
BioSample SAMN02196905

Supplementary file Size Download File type/resource
GSM694155_LUN.bowtie.gz 202.7 Mb (ftp)(http) BOWTIE
Processed data provided as supplementary file

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