|
| Status |
Public on Jun 21, 2016 |
| Title |
Alp13-del_H4K20me1 ChIP-seq 2 |
| Sample type |
SRA |
| |
|
| Source name |
yeast cells
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
genotype: ura4-D18 leu1-32
antibody: H4K20me1
|
| Growth protocol |
Histone trunover experiment : Grow up cells in 4% sucrose PMG medium at 37°C ChIP-seq and mRNA-seq : Grow up cells in YES medium at 37°C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-seq libraries for genome-wide sequencing were prepared using 10 ng of input DNA or 1 to 10 ng of eluted ChIP DNA using NEXTflex ChIP-Seq kit, Bioo Scientific (cat.5143). mRNA-seq libraries were made using NEXTflexTM Rapid RNA-Seq kit (cat. 5138) from isolated mRNA.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
G2_Alp13d_H4K20me1_H3.bed
|
| Data processing |
Prepared libraries were sequenced on a HiSeq2500 with single-end method (50-bp reads).
ChIP-seq reads were aligned to the S.pombe genome (ASM294v2) using NovoAlign (Novocraft technologies, Malaysia).
Significantly enriched peaks were identified using Homer and mapped reads were quantified using DeepTools and bwtool.
For mRNA-seq analysis, raw reads were aligned to S. pombe genome (ASM294v2) using STAR aligner.
The number of mapped reads was further analyzed using HOMER and DESeq
Genome_build: S. pombe EF2 genome assembly; ASM294v2
Supplementary_files_format_and_content: RNA-seq : tab-delimited text files include RPKM values for each Sample, ChIP-seq : bed files including peak position
|
| |
|
| Submission date |
Jun 20, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Yoonjung Choi |
| E-mail(s) |
[email protected]
|
| Organization name |
KAIST
|
| Street address |
291 Daehak-ro, Yuseong-gu
|
| City |
Daejeon |
| ZIP/Postal code |
34141 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL17225 |
| Series (1) |
| GSE83538 |
Both H4K20 mono-methylation and H3K56 acetylation mark transcription-dependent histone turnover in fission yeast |
|
| Relations |
| BioSample |
SAMN05275959 |
| SRA |
SRX1867592 |
