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Sample GSM2700714

Query DataSets for GSM2700714

Status

Public on Jan 02, 2018

Title

ko6B_ATAC-seq

Sample type

SRA

Source name

yeast

Organism

Saccharomyces cerevisiae

Characteristics

genotype: CEN.PK ARP5::KAN
growth phase: RB late

Growth protocol

Yeast grown in continuous culture to induce metabolic cycling; samples taken at different times across these metabolic cycles. The growth stages are described in Kuang, Z., Cai, L., Zhang, X., Ji, H., Tu, B.P., and Boeke, J.D. (2014). High-temporal-resolution view of transcription and chromatin states across distinct metabolic states in budding yeast. Nat Struct Mol Biol 21, 854 863. Samples A and B are technical replicates-- RNA was prepared separately from the same culture.

Extracted molecule

genomic DNA

Extraction protocol

yeast were harvested and processed immediately as described in the method sections.

Library strategy

ATAC-seq

Library source

genomic

Library selection

other

Instrument model

Illumina NextSeq 500

Description

processed data file:
normalized_atac_counts.csv

Data processing

Reads were aligned using Bowtie2. Duplicate reads were removed using Picard tools and replicates were combined for analysis.ATAC-seq signal in promoters was quantified as the number of fragments mapping to the window 400bp upstream to 100bp downstream from the TSS. NucleoATAC and chromVAR were used to assess promoter accessibility and nucleosome positioning resectively.
genome build: sacCer3 (April 2011)
processed data files format and content: Fragments mapped to promoters

Submission date

Jul 12, 2017

Last update date

Jan 03, 2018

Contact name

Graeme Gowans

E-mail(s)

[email protected]

Organization name

Stanford University

Department

Biology