|
| Status |
Public on Jul 13, 2017 |
| Title |
Input for Cnd2 ChIP |
| Sample type |
SRA |
| |
|
| Source name |
mitosis
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: YUK421 Cnd2-HA
cell cycle stage: mitosis
treatment: 5 µg/mL thiamine
|
| Treatment protocol |
Mitotic arrested cells were crosslinked with 0.5 % formaldehyde for 30 minutes at 25 ºC
|
| Growth protocol |
Cells were grown in EMM supplemented with glutamate. Cells were arrested in mitosis by addition of 5 µg/mL of thiamine.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Crosslinked chromatin was immunoprecipitated with anti-HA antibody.
NEBNext Ultra DNA Library Prep kit for Illumina and NEBNext Multiplex Oligos for Illumina (Index Primers Set 1) were used for adapter ligation and indexing. Indexed Hi-C library was purified by double selection of SPRI selection beads.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Control for ChIP-seq
Condensin_peaks.xls
|
| Data processing |
Trimming. Read 1 and read 2 files were trimmed to 50bp
Alignment. Each read in the pair was independently aligned to build ASM294v2.21 of the Pombe genome using the BWA-mem algorithm (version 0.7.12).
Peak identification. Peaks were indentified using Macs2 (version 2.1.0) using the paired input sample as control.
Genome_build: ASM294v2.21
Supplementary_files_format_and_content: An excel spreadsheet summarising parameters and identified ChIP peaks.
|
| |
|
| Submission date |
Feb 03, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Yasutaka Kakui |
| E-mail(s) |
yasukakui@aoni.waseda.jp
|
| Organization name |
Waseda Institute for Advanced Study
|
| Street address |
1-21-1 Nishiwaseda, Shinjuku-ku
|
| City |
Tokyo |
| ZIP/Postal code |
169-0051 |
| Country |
Japan |
| |
|
| Platform ID |
GPL13988 |
| Series (2) |
| GSE94474 |
Condensin-mediated remodeling of the mitotic chromatin landscape in fission yeast |
| GSE94478 |
Condensin-mediated remodeling of the mitotic chromatin landscape in fission yeast |
|
| Relations |
| BioSample |
SAMN06294190 |
| SRA |
SRX2536769 |
