|
Status |
Public on Feb 02, 2021 |
Title |
set1_B |
Sample type |
SRA |
|
|
Source name |
set1_nucleosome core particles (MNase)
|
Organism |
Saccharomyces cerevisiae |
Characteristics |
strain: YPE602 genotype: MATa ade2-1 can1-100 leu2-3,112 trp1-1 ura3-1 HIS3+ RAD5+ set1::NAT1
|
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 |
E-mail(s) |
erikssop@mail.nih.gov
|
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 |
|
Relations |
BioSample |
SAMN15814571 |
SRA |
SRX8945033 |