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Sample GSM4192734

Query DataSets for GSM4192734

Status

Public on Jun 18, 2020

Title

WT_Pol II_rapa_ChipSeq_rep1

Sample type

SRA

Source name

yeast cells

Organism

Saccharomyces cerevisiae

Characteristics

strain: BY4741
genotype: wild type
treatment: rapamycin treatment
chip antibody: Pol II (Santa Cruz, 56767, lot AB_C1017

Extracted molecule

genomic DNA

Extraction protocol

After beads beating, chromatin was sonicated. Then cell lysates were centrifuged to pellet debris. Immunoprecipitation was performed overnight with antibody.
The ChIP-seq libraries were prepared using VAHTSTM Universal DNA Library Prep Kit for Illumina® V3 (Vazyme). The quality and quantity of constructed libraries were determined using Fragment Analyzer (Advanced Analytical).

Library strategy

ChIP-Seq

Library source

genomic

Library selection

ChIP

Instrument model

Illumina NovaSeq 6000

Data processing

Low quality reads and adaptor contamination were removed by Trimmomatic v0.38
For RNA-Seq, the filtered reads were mapped to SacCer3 using STAR v2.5.3a. For ChIP-Seq, the filtered reads were aligned against SacCer3 genome using Bowtie2 v2.3.4.3 with default parameters.
For RNA-Seq, the mapped reads was quantified using featureCounts v1.6.3. Reads count normalization and differential gene expression analysis was performed using DESeq2 v1.24.0. For ChIP-Seq, MACS2 v2.2.1 with a P value threshold of 1e -5 was used to call ChIP peaks.
Genome_build: SacCer3
Supplementary_files_format_and_content: reads were quantified using featureCounts v1.6.3

Submission date

Nov 26, 2019

Last update date

Jun 18, 2020

Contact name

shu Wenjie

E-mail(s)

shuwenjie@whu.edu.cn

Phone

17671613819

Organization name

Wuhan University