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Sample GSM7471017 Query DataSets for GSM7471017
Status Public on Apr 21, 2024
Title 1_a-Set1_WT_strain_rep1
Sample type SRA
 
Source name MATa his3∆0 leu2∆0 met15∆0 ura3∆0
Organism Saccharomyces cerevisiae
Characteristics chip antibody: Set1
genotype: MATa his3{delta}0 leu2{delta}0 met15{delta}0 ura3{delta}0
Treatment protocol Before wash the cells with 1XTBS, cells were treated with 1% formaldehyde for 5mins and quenched with 2.5M Glycine for 20mins
Growth protocol Cells were prepared from exponentially growing at OD600=1.0. Harvested cells were resuspended with 4ml of 1XTBS and evenly divided into 4 eppendorf tubes. Cell is harvested by Centrifuge 3000 rpm 5min and supernatant was removed. After one more wash step, samples were stored at -80℃.
Extracted molecule genomic DNA
Extraction protocol Cells were resuspended with lysis buffer and homogenized with glass beads at cold room. Lysed cells were sonicated and centrifuged to obtain soluble chromatin fraction. S.cerevisiae chromatin lysates, containing 5% C.albicans Δset1 chromatin extract for control of sample-to-sample normalization, were incubated with antibody and antibody-protein-chromatin complex was captured by Protein A/G agarose. After sequential washing steps and reverse crosslinking, remaining DNA is purified by phenol-chloroform extraction and washing.
ChIP-Seq DNA samples were quantified by Quant-iT PicoGreen dsDNA Assay kit and their quality were assessed Bioanalyzer 2100. ChIP-Seq library was constructed with TruSeq ChIP Sample Prep Kit (Illumina) according to manufacturer’s instructions.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
Data processing The sequencing adapter removal and quality-based trimming on raw data was performed by Trimmomatic v. 0.36 with TruSeq adapter sequences.
Cleaned reads were mapped to reference genome using bowtie v2.4.2 with default parameter
For normalization, C. albicans spike-in reads in each sample was calculated.
We assumed that the amount of spike-in added to each sample is same, and the normalization ratio was calculated as "1000000/spike-in reads" for each sample.
The normalized bedGraph was produced by using 'bamCoverage --scaleFactor' and calculated normalization ratio.
BedGraph files were converted to BigWig files and the resulted bw files were averaged by WiggleTools 1.2 (https://github.com/Ensembl/WiggleTools).
Assembly: Saccharomyces cerevisiae S288C genome assembly R64 (sacCer3)
Supplementary files format and content: bigwig
 
Submission date Jun 09, 2023
Last update date Apr 22, 2024
Contact name Junsoo Oh
E-mail(s) ohjunsu1007@naver.com
Organization name Kangwon National University
Street address Kangwondaehakgil-1
City Chuncheon
ZIP/Postal code 24341
Country South Korea
 
Platform ID GPL17342
Series (1)
GSE234564 Swd2/Cps35 determines H3K4 tri-methylation via interactions with Set1 and Rad6_Chromatin occupancy of Set1 in several strains
Relations
BioSample SAMN35687315
SRA SRX20648678

Supplementary file Size Download File type/resource
GSM7471017_1_a-Set1_WT_minus_deltaset1_mean.bw 1.9 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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