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Sample GSM994401 Query DataSets for GSM994401
Status Public on Oct 02, 2012
Title Mit1-del_MNaseSeq
Sample type SRA
 
Source name Mit1-del_MNaseSeq
Organism Schizosaccharomyces pombe
Characteristics genotype: ade6-M210 leu1-32 ura4-D18
Growth protocol Grow up cells in YES medium at 30°C
Extracted molecule genomic DNA
Extraction protocol Cells were suspended in 200 ml of culture medium at a density of 2x107 cells/ml, and then cross-linked with formaldehyde (final concentration of 1% v/v) for 15 minutes at room temperature. The fixed cells were subjected to chromatin isolation and MNase digestion as described above(Bernardi et al., 1991). Pelleted nuclei were digested with 600 U of micrococcal nuclease (NEB) at 37°C for 20 min, and samples were subjected to proteinase K treatment followed by overnight de-cross-linking at 65°C. Naked DNA was prepared from genomic DNA digested with 100 U of micrococcal nuclease. Mono-nucleosomal fragments were gel purified from 1.5% agarose gels run in TAE, and DNA was extracted with QIAGEN gel extraction kits and subject to paired end sequencing using the Illumina platform.
 
Library strategy MNase-Seq
Library source genomic
Library selection MNase
Instrument model Illumina HiSeq 2000
 
Data processing MNase-seq reads were aligned to the S.pombe (EF2) genome assembly using the Bowtie alignment program (Langmead et al., 2009).
The center of fragments was calcualted from paired-end reads and the fragment size was set to 140 bp.
The fragments were normalized and processed by the nucleR program (Flores & Orozco, 2011).
Genome_build: EF2
Supplementary_files_format_and_content: wig files were generated using the nucleR program.
 
Submission date Aug 29, 2012
Last update date May 15, 2019
Contact name Yoonjung Choi
E-mail(s) handygirl81@gmail.com
Organization name Korea Advanced Institute of Science and Technology
Street address 291 Daehak-ro, Yuseong-gu
City Daejeon
ZIP/Postal code 305-701
Country South Korea
 
Platform ID GPL13988
Series (2)
GSE40451 Hrp3 controls nucleosome positioning to suppress non-coding transcription in eu- and heterochromatin [MNase-Seq]
GSE40453 Hrp3 controls nucleosome positioning to suppress non-coding transcription in eu- and heterochromatin
Relations
SRA SRX181324
BioSample SAMN01141244

Supplementary file Size Download File type/resource
GSM994401_mit1.wig.gz 51.0 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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