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Sample GSM4727133 Query DataSets for GSM4727133
Status Public on Feb 02, 2021
Title ioc4_B
Sample type SRA
Source name ioc4_nucleosome core particles (MNase)
Organism Saccharomyces cerevisiae
Characteristics strain: YPE608
genotype: MATa ade2-1 can1-100 leu2-3,112 trp1-1 ura3-1 HIS3+ RAD5+ ioc4::hph1
Growth protocol Wild-type cells and null mutants were grown to mid-log phase in synthetic complete medium containing 40mg per liter adenine and 2% glucose.
Extracted molecule genomic DNA
Extraction protocol Nuclei were prepared from unfixed yeast cells and then digested with MNase.
The DNA was repaired using the DNA repair kit from New England Biolabs (NEB). The repaired DNA was processed for paired-end sequencing according to the Illumina protocol. NEB kits# M0309L, E7370L , E7335L, E7500L were used.
Library strategy MNase-Seq
Library source genomic
Library selection MNase
Instrument model Illumina HiSeq 1000
Description Biological replicate 2
Data processing Sequencing data was aligned to the yeast genome (SacCer3) using Bowtie2 with default settings. Occupancy profiles in bedGraph format were generated using bedtools. For further analyses the aligned reads were size-selected as described in the article.
Genome_build: Genome_build: SacCer3
Supplementary_files_format_and_content: bedgraph format
Submission date Aug 13, 2020
Last update date Feb 03, 2021
Contact name Peter Eriksson
Phone 3014514670
Organization name National Institutes of Health
Department NICHD
Street address 9000 Rockville Pike, Bldg.6A/2A14
City Bethesda
State/province Maryland
ZIP/Postal code 20892
Country USA
Platform ID GPL17582
Series (1)
GSE156224 The yeast ISW1b ATP-dependent chromatin remodeler is critical for nucleosome spacing and dinucleosome resolution
BioSample SAMN15814576
SRA SRX8945029

Supplementary file Size Download File type/resource
GSM4727133_ioc4_B.bedgraph.gz 52.8 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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