GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM1621333

Query DataSets for GSM1621333

Status

Public on Apr 22, 2015

Title

S. cerevisiae lin6c

Sample type

SRA

Source name

Saccharomyces cerevisiae cells

Organism

Saccharomyces cerevisiae

Characteristics

strain: GSY157
growth stage: mid-log
treatment: none

Treatment protocol

none

Growth protocol

Cells were grown to mid-log phase in YPD

Extracted molecule

genomic DNA

Extraction protocol

5 million cells were washed twice in Sorbitol buffer (1.4 M Sorbitol, 40 mM HEPES-KOH pH 7.5, 0.5 mM MgCl2) before being incubated for 30 min at 30 degrees and shaking at 300 rpm with 0.5 mg/mL 100T zymolyase. The cells were then washed twice in Sorbitol Buffer before being incubated with 2.5 ml of Nextera Transposase in 47.5 ml of 1x TD buffer at 37 degrees for 30 minutes.
Sequencing libraries were constructed using a modified version of the Illumina Nextera DNA Sample prep kit, as per Buenrostro et al. (2013).

Library strategy

OTHER

Library source

genomic

Library selection

other

Instrument model

Illumina HiSeq 1000

Description

S. cerevisiae ATAC-seq sample. Four populations of S. cerevisiae strain GSY14744 were used, with three of the four populations (lin2, lin3, and lin6) derived from the first (lin0) and differing only in that they were grown on plates for 200 generations in conditions to minimize selective pressures.
processed data files: lin_all.nucpos.bed, lin_all.nucsig.bw, lin_all.occ.bw, sacCer3.scores.bw, sacCer3.mappable.bed

Data processing

Library strategy: ATAC-seq

Adapters were trimmed from reads before alignment using bowtie 2 with the -X 2000 flag. Duplicate fragments for each sample were discarded, as were reads mapping to chrM, reads with mapping quality less than 30, and reads that were not properly paired.

Nucleosome calling was performed in broad open chromatin regions determined using MACS2 and filtered for high mappability. For the osmotic stress time-course, nucleosome calling was performed in regions around TSS that overlapped with broad open chromatin peaks in at least one time point.

genome build: sacCer3 for S. cerevisiae, ASM294v2.21 for S. pombe, and hg19 for human GM12878

processed data files format and content: *.nucpos.bed.gz files contain nucleosome positions. Columns are as follows: 1) chromosome 2) dyad position (0-based) 2) dyad position (1-based) 3)

processed data files format and content: *.nucleoatac_signal.bw are BigWig files containing the normalized NucleoATAC signal

processed data files format and content: *.occ.bw are BigWig files contining the nucleosome occupancy

processed data files format and content: *.peaks.final.bed are highly mappable open chromatin regions for which nucleosome calling was performed. For the osmotic stress time course, analyis was performed on regions around tss that overlapped with peaks (osmotic.tss_peak_regions.bed).

processed data files format and content: *.Scores.bw are BigWig files that contain transposase preference scores used in the sequence bias normalization for nucleosome calling. These scores represent the log of the relative probability of insertion.

Submission date

Feb 27, 2015

Last update date

May 15, 2019

Contact name

William J Greenleaf

E-mail(s)

wjg@stanford.edu

Organization name

Stanford University

Department

Genetics