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Sample GSM6337017

Query DataSets for GSM6337017

Status

Public on Oct 18, 2023

Title

S228Arep1

Sample type

SRA

Source name

S288C

Organism

Saccharomyces cerevisiae S288C

Characteristics

strain: S288C
genotype: Set1 S228A

Treatment protocol

No treatment

Growth protocol

Cells were grown in YPD until mid-log phase

Extracted molecule

total RNA

Extraction protocol

Lysates were clarified from sonicated yeast cell pellets and histone-DNA complexes were isolated with antibody against H3 (ab1791, Abcam),H3K4me3 (Abclonal; A2357),FLAG (F1804-1MG; Sigma-Aldrich),Rpd3 (sc-514160; Santa Cruz Biotechnology)
Libraries were prepared using the HTP KAPA kit

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Data processing

Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to sacCer3 whole genome using bowtie v0.12.2 with parameters -q -p 5 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: sacCer3

Submission date

Jul 13, 2022

Last update date

Oct 18, 2023

Contact name

Yu Qi

Organization name

Hubei university

Department

College of life sciences

Street address

xujiapeng