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Sample GSM2476216 Query DataSets for GSM2476216
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
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
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
BioSample SAMN06294190
SRA SRX2536769

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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