|
Status |
Public on Apr 24, 2012 |
Title |
Log Fixed 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: Fixed 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 (5-8Ã106 cells/ml ) or stationary phase (1-2Ã108 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 Fixed 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 |
SAMN02196903 |