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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
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
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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