|
| Status |
Public on Aug 01, 2024 |
| Title |
1_BY4741-1-H3K4me3 |
| Sample type |
SRA |
| |
|
| Source name |
cells
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
tissue: cells
chip antibody: H3K4me3
genotype: MATa his3delta0 leu2delta0 met15delta0 ura3delta0
|
| 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% of Schizosaccharomyces pombe 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, S. pombespike-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: fastq, bigwig
|
| |
|
| Submission date |
Oct 05, 2023 |
| Last update date |
Aug 01, 2024 |
| Contact name |
Shinae Park |
| E-mail(s) |
[email protected]
|
| Organization name |
Kangwon National University
|
| Street address |
Kangwondaehak-gil
|
| City |
Chuncheon-si |
| ZIP/Postal code |
KS007 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL17342 |
| Series (2) |
| GSE244733 |
Leo1 and Set1-mediated H3K4me3 contribute to sterol homeostasis in yeast [ChIPseq] |
| GSE244789 |
Leo1 and Set1-mediated H3K4me3 contribute to sterol homeostasis in yeast |
|
| Relations |
| BioSample |
SAMN37700056 |
| SRA |
SRX22005901 |
